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标题: 使用 sobtop 被审稿人问了该怎么回答 [打印本页]

作者
Author: KikuYoung 时间: 2025-8-5 20:36
标题: 使用 sobtop 被审稿人问了该怎么回答
各位老师好，在分子动力学模拟工作中，我使用 Sobtop 生成了铁卟啉的拓扑，并使用 Multiwfn 拟合了 RESP 电荷。被审稿人询问了，不知道群里老师有没有相关应对经验。
- How were the RESP charges computed in Multiwfn? Which fittingalgorithm etc. was utilized? How were the charges made compatible with AMBER?
- Why did the authors choose to use Multiwfn for RESP chargecomputations instead of the native AMBER program Antechamber which can alsocompute RESP charges from ESP calculations with Gaussian. Likewise, why was the‘sobtob’ tool utilized instead of Antechamber
Multiwfn 的 RESP 计算流程就是标准的计算流程，难道就把标准方法写一遍？我模拟使用 GROMACS，力场是 ff14SB。

作者
Author: sobereva 时间: 2025-8-5 22:14
让他看Multiwfn手册3.9.16节，对RESP拟合过程交代得超级细致，默认设置下和RESP原文的流程完全一样

antechamber没法算带有铁的物质的RESP电荷，局限性极大，远不如Multiwfn普适和灵活，自然当前需要用Multiwfn

PS：用Multiwfn算RESP电荷的文章有几百篇了，充分证明了Multiwfn算RESP电荷的合理性和流行度。其中的一部分文章（Google学术搜文章标题可找到）：
A General Nonbonded Force Field Based on Accurate Quantum Mechanics Calculations for Elements H–La and Hf–Rn
A molecular dynamics study of the binding effectiveness between undoped conjugated polymer binders and tetra-sulfides in lithium–sulfur batteries
A Multiscale Simulation Study of Influence of Morphology on Ion Transport in Block Copolymeric Ionic Liquids
A phenylalanine dynamic switch controls the interfacial activation of Rhizopus chinensis lipase
A polymer acceptor with double-decker configuration enhances molecular packing for high-performance all-polymer solar cell
A quantum-chemistry and molecular-dynamics study of non-covalent interactions between tri-n-butyl phosphate and 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide
Achieving high-voltage polymer-based all solid-state batteries based on thermodynamic and kinetic degradation insights
Acidified glycerol as a one-step efficient green extraction and preservation strategy for anthocyanin from blueberry pomace
Adsorption behaviors of ethyltriethoxysilane on the calcium silicate hydrate surface-Effect of Ca-Si ratio and adsorption sites
Advancing lithium metal electrode beyond 99.9_ coulombic efficiency via super-saturated electrolyte with compressed solvation structure
All-Liquid-Phase Reaction Mechanism Enabling Cryogenic Li–S Batteries
Allosteric site identification, virtual screening and discovery of a sulfonamide Hsp110-STAT3 interaction inhibitor for the treatment of hypoxic pulmonary arterial hypertension
An Ab Initio Study of the Effect of Strain on the Permeability of N2 and CO2 in N-Graphdiyne
Analysis and intensification of energy saving process for separation of azeotrope by ionic liquid extractive distillation based on molecular dynamics simulation
Analysis of SO2 Physisorption by Edge-Functionalized Nanoporous Carbons Using Grand Canonical Monte Carlo Methods and Density Functional Theory
Application of Imidazolium-based Polyionic Liquids to Separate the 1,3,5-Trioxane-Water-Ethanol-Water System Based on Experimental Verification and Molecular Mechanism Analysis
Application of Molecular dynamics-based pharmacophore and machine learning approach to identify novel Mcl1 inhibitors
Approaching the Dimerization Mechanism of Small Molecule Inhibitors Targeting PD-L1 with Molecular Simulation
Asymmetric Coordination Engineering Accelerates the Electrochemical Nitrate Reduction Kinetics on Metal-organic Frameworks
Atomic insights into the sintering process of polycyclic aromatic hydrocarbon clusters
Autocatalytic Mechanism Induced by NO2– Ion with Effect of Proton-Coupled Electron Transfer in Early Pyrolysis of Azacyclo-Nitramine Compounds RDX
Benchmarking Classical Molecular Dynamics Simulations for Computational Screening of Lithium Polymer Electrolytes
Bifunctional self-segregated electrolyte realizing high-performance zinc-iodine batteries
Bioinspired Janus starch film with dual functionality via citral nanoemulsion-mediated interfacial self-assembly for fresh-cut fruits and vegetables preservation
Boosting the hole transport of conductive polymer by regulating the ion ratio in ionic liquid additive
BP[dG]-induced distortions to DNA polymerase and DNA duplex-A detailed mechanism of BP adducts blocking replication
Cation‐dipole Interaction that Creates Ordered Ion Channels in an Anion Exchange Membrane for Fast OH- Conduction
Comprehensive analysis of lignin dimer dissolution microscopic mechanism in different aromatic-based deep eutectic solvent
Computational assessment of herbal medicine-derived compounds as potential inhibitors of SARS-CoV-2 main protease
Computational Discovery of RSV Pre-F Inhibitors via Reinforcement Learning-Driven ab Initio Design from Natural Fragment Libraries
Computational Insights into Acrylamide Fragment Inhibition of SARS-CoV-2 Main Protease
Computational studies of the encapsulation of ibuprofen and paracetamol into cucurbit[7]uril
Computational Study of the Electrostatic Potential and Charges of Multivalent Ionic Liquid Molecules
Computer-driven Evolution of Myrosinase from the Cabbage Aphid for Efficient Production of (R)-Sulforaphane
Concretized structural evolution supported assembly-controlled film-forming kinetics in slot-die coated organic photovoltaics
CONI-Net-Machine Learning of Separable Intermolecular Force Fields
Construction and Properties of O-W Liquid Crystal Nanoemulsion
Coordination Symmetry Breaking of Single Atom Catalysts for Robust and Efficient Nitrate Electroreduction to Ammonia
Data-Assisted Design of Temperature-Resistant Weakly Solvating Electrolyte for All-Climate 500 Wh kg Lithium-Metal Batteries
Data-Driven Parametrization of All-atom force fields for Organic Semiconductors
Deformation constraints of graphene oxide nanochannels under reverse osmosis
Density of States Engineering of n-Doped Conjugated Polymers for High Charge Transport Performances
Design and optimization of reactive dividing-wall extractive distillation process for dimethyl carbonate synthesis based on quantum chemistry and molecular dynamics calculation
Design of dual-electrode interfacial kinetics regulator for long-lasting Ah-level zinc-iodine batteries
Design, Synthesis, and Bioactivities of N-Heterocyclic Ureas as Strigolactone Response Antagonists against Parasitic-Weed Seed Germination
Design, Synthesis, Antifungal Evaluation, and Action Mechanism of Novel l-Carvone-Based Derivatives as Potential Succinate Dehydrogenase Inhibitors
Development and mechanistic insights into a novel deep eutectic solvent-based aqueous two-phase system for sustainable recovery
Development of human lactate dehydrogenase a inhibitors-high-throughput screening, molecular dynamics simulation and enzyme activity assay
Diamine alkanes as a new kind of organic phase change materials with unusually high energy density
Discovery of 2,4-diphenyl-substituted thiazole derivatives as PRMT1 inhibitors and investigation of their anti-cervical cancer effects
Disentangling Energy Transfer Pathways in Donor–Acceptor Dyads-A Molecular-Level Perspective for TADF OLED Applications
Distribution of potassium perfluoro (2-ethoxyethane) sulfonate in NaCl solution-insights from molecular dynamics simulation
Dual-bioinspired and ultra-flexible photothermal eutectogels for highly efficient passive anti-freezing
Effect of combined ultra-high pressure gallic acid cochromism on the stability of Aronia melanocarpa anthocyanins in juice systems
Effect of PO43- on the polymerization of polyferric phosphatic sulfate and its flocculation characteristics for different simulated dye wastewater
Effect of side chain on the electrochemical performance of poly (ether ether ketone) based anion-exchange membrane-A molecular dynamics study
Effects of C-ring structures on the formations of flavonoid semiquinones and their binding behavior with β-lactoglobulin as revealed by experimental and modeling approaches
Effects of modification modules-adjusted intermolecular forces on docetaxel prodrug Nanoassemblies-From assembly mechanisms to in vivo fate
Effects of Molecular Weight and Orientation on the Membrane Permeation and Partitioning of Polycyclic Aromatic Hydrocarbons-A Computational Study
Efficient extraction of Au(Ⅲ) by a piperidine-based ionic liquid and exploration of the mechanism driving force
Efficient lamellar two-dimensional proton channels derived from dipole interactions in a polyelectrolyte membrane
Efficient synthesis of bepotastine and cloperastine intermediates using engineered alcohol dehydrogenase with a hydrophobic pocket
Electronic structures of zwitterionic and protonated forms of glycine betaine in water-Insights into solvent effects from ab initio simulations
Enhanced F-Gases’ Recovery by Introducing Lewis Acid Sites into MFI Zeolites
Enhanced performance in lithium metal batteries-A dual-layer solid electrolyte interphase strategy via perfluoropolyether derivative additive
Enhanced steric effect and desolvation process on organic solvent nanofiltration-A mechanism study for removing anionic dyes
Enhancing sCO2 nano-emulsion stability with trisiloxane surfactants for CCUS
Enhancing selective adsorption of CO2 through encapsulating FeTPPs into Cu-BTC
Experimental and Quantum Chemical Calculations on the High-Efficiency Transesterification of Dimethyl Carbonate with Alcohol Catalyzed by Calcium Oxide
Experimental and simulation studies on the simultaneous removal of methanol and water from dimethyl ether crude gas by choline-based deep eutectic solvents
Exploration of the Multiscale Interaction Mechanism between Natural Deep Eutectic Solvents and Silybin by QC Calculation and MD Simulation
Exploring Product Release from Yeast Cytosine Deaminase with Metadynamics
Exploring the Molecular Basis of Substrate and Product Selectivities of Nocardicin Bifunctional Thioesterase
Exploring the molecular mechanism of ginseng against anthracycline-induced cardiotoxicity based on network pharmacology, molecular docking and molecular dynamics simulation
Extraction and interaction insights for enhanced separation of phenolic compounds from model coal tar using a hydroxyl-functionalized ionic liquid
Extraction and mechanism exploration for separating cresols from coal tar by ionic liquid ethanolamine lactate
Extraction of chlorogenic acid from Lonicera japonica Thunb. using deep eutectic solvents
Extraction of curcumin from turmeric rhizome utilized by a surfactant-free microemulsion based on deep eutectic solvent
Facile fabrication of fluorine-free photo-thermal super-hydrophobic coating with hierarchical structure for efficient anti-icing and de-icing applications
Force field benchmark of asphalt materials-Density, viscosity, glass transition temperature, diffusion coefficient
Gaseous Cyclodextrin-closo-Dodecaborate Complexes ΧCD·[B12X12]2- (Χ = α, β, γ; X = F, Cl, Br, I)-Electronic Structures and Intramolecular Interactions
Green and low-viscosity deep eutectic solvents for the extraction of quinoline from wash oil
Heterogenous Chemistry of I2O3 as a Critical Step in Iodine Cycling
High adhesion hydrogel electrolytes enhanced by multifunctional group polymer enable high performance of flexible zinc-air batteries in wide temperature range
High-valent iron-oxo species mediated cyclic oxidation through single-atom triple bondFe-N6 sites with high peroxymonosulfate utilization rate
Highly cost-effective wheat starch-stearic acid complexes enabled by microwave processing
Highly efficient separation of benzene + cyclohexane mixtures by extraction combined extractive distillation using imidazolium-based dicationic ionic liquids
Hydrotropic solubilization of zinc acetates for sustainable aqueous battery electrolytes
Identification of RdRp-NiRANJAK1 Dual-Target Drugs for COVID-19 Treatment
Impact of Confinement and Zwitterionic Ligand Chemistry on Ion–Ion Selectivity of Functionalized Nanopores
Impact of Glycosylation of Apolipoprotein D on Its Interaction with Gold Nanoparticles
Impact of Nitrogen-to-Phosphorus Substitution on End Group of the Y6 Nonfullerene Molecule for Organic Photovoltaics
In silico approaches for the identification of novel ULK1 inhibitors-pharmacophore model, molecular docking and molecular dynamics simulations
In silico study of the encapsulation of α-tocopherol and α-tocotrienol vitamins E into cucurbit[7]uril
In Situ Fabricated Quasi-Solid Polymer Electrolyte for High-Energy-Density Lithium Metal Battery Capable of Subzero Operation
In situ valence-transited arsenic nanosheets for multi-modal therapy of colorectal cancer
In-situ Water Separation Enhanced Methyl Glycolate Oxidation to Methyl Glyoxylate by Catalytic Membrane Reactor
Influence of Chemical Structure of Fluorinated Surfactants on the Air-Water Interface Properties
Insight into structural properties of polyethylene glycol monolaurate in water and alcohols from molecular dynamics studies
Insights into Lewis-Br?nsted acidity of metal chlorides and solvent effect of alcohols for synthesis of γ-valerolactone
Insights into the mechanism during viscosity reduction process of heavy oil through molecule simulation
Interfacial characteristics and foam stability-A microscopic perspective from molecular dynamics simulation
Intermolecular Interaction and Extraction Explorations for Separation of High-Boiling Neutral Nitrogen Compounds Using Biodegradable Ionic Liquids
Investigating the Distribution of Potassium Perfluoro (2-Ethoxyethane) Sulfonic Acid in WaterGas Systems using Molecular Dynamics Method
Ionic liquid decoration for hole transport improvement of PEDOT
Ion–solvent chemistry in lithium battery electrolytes-From mono-solvent to multi-solvent complexes
ITGA4 Contributes to 5-Fluorouracil Resistance by Up-Regulating PI3KAKT Signaling
Learning protein-ligand unbinding pathways via single-parameter community detection
LiNO3-Based Electrolyte with Fast Kinetics for Lithium Metal Batteries Under Practical Conditions
Low-Temperature and High-Voltage Lithium-Ion Battery Enabled by Localized High-Concentration Carboxylate Electrolytes
Machine learning methods for developments of binding kinetic models in predicting protein-ligand dissociation rate constants
Mechanism of Deep Eutectic Solvent Delignification-Insights from Molecular Dynamics Simulations
Mechanism of High Hydrocarbon-Fuel-Gelation Performance of Ultralow-Concentration Bis-urea-Based Gellants
Mechanisms of ion transport in lithium salt-doped polymeric ionic liquid electrolytes at higher salt concentrations
Mechanistic Insights into Chloric Acid Production by Hydrolysis of Chlorine Trioxide at an Air–Water Interface
Micro-Aqueous Organic System-A Neglected Model in Computational Lipase Design？
Microscopic insights into viscosity reduction mechanisms in metal-containing heavy oil
Microscopic Mechanism of the Polyacrylamide Hydrophilic Chain on Nanoemulsion-Based Carbon Geological Sequestration
Microscopic Mechanisms of Reaction-Coupled Acid Diffusion in Chemically Amplified Photoresists
Microscopic Understanding of The Supramolecular Interaction in Enhanced Oil Recovery
Mix-Charged Nanofiltration Membrane for Efficient Organic Removal from High-Salinity Wastewater
Molecular and experimental insights into the inhibition effects of chitosan biguanidine on the kinetic and agglomeration of gas hydrates
Molecular docking with conformer-dependent charges
Molecular Dynamics Analysis of Li+ Mg2+ Transport Mechanism in COF Membranes with Flexible Oxygen-Containing Side Chains
Molecular dynamics interpretation of citric acid-water assisting mechanism in deep eutectic solvent to destruct agricultural residue
Molecular dynamics simulation of CO2 in organic solvent and polymer–solvent solutions
Molecular dynamics simulation of potassium perfluorooctanesulfonate at the oil-water interface
Molecular dynamics simulation study on behavior of modified polyacrylamide reducing oil-water interfacial tension
Molecular dynamics simulations of choline chloride and ascorbic acid deep eutectic solvents-Investigation of structural and dynamics properties
Molecular Dynamics Study of Silica Nanoparticles and CO2-Switchable Surfactants at an Oil–Water Interface
Molecular Dynamics Study on Adsorption and Desorption of the Model Oligosaccharide above Polymer Antifouling Membranes
Molecular dynamics study on self-assembled dodecylphosphocholine nanomicelles used as drug delivery system for carrying curcumin
Molecular dynamics study on the anomalous behavior of phase transition heats of alcohols at vapor-liquid interface
Molecular dynamics study on the structure and antifouling performance of aromatic polyamide membrane with sulfonamide group
Molecular encapsulation of 5, 10, 15, 20-tetrakis (4-methylphenyl) porphyrinato iron (III) chloride (FeTPP) into MIL-101(Cr) for superior CO2-N2 separation performance
Molecular insight into the reversible dispersion and aggregation of graphene utilizing photo-responsive surfactants
Molecular Insights into Cyclodextrin–Adamantane-Modified Copolymer Host–Guest Interactions
Molecular interaction induced dual fibrils towards organic solar cells with certified efficiency over 20%
Molecular interaction mechanism and process analysis of separation of cyclohexane-ethyl acetate by extractive distillation
Molecular Mechanism and Absorption Performance Evaluation of CO2 Capture from the PCC Process by Monoethanolamine-Based Deep Eutectic Solvents
Molecular mechanism and extraction performance evaluation of diethylene glycol-based DES for extraction desulfurization process of fuel oil
Molecular simulation and optimization of extractive distillation for separation of dimethyl carbonate and methanol
Molecular simulation combined with DFT calculation guided heteroatom-doped biochar rational design for highly selective and efficient CO2 capture
Molecular simulations of the effects of substitutions on the dissolution properties of amorphous cellulose acetate
Morphology prediction of dihydroxylammonium 5,5′-bistetrazole-1,1′-diolate (TKX-50) crystal in different solvent systems using modified attachment energy model
Multi-Hydration Induced Zwitterionic Hydrogel with Open Environment Stability for Chemical Sensing
Multifunctional nano-metal chelate for orchestrated chemo-chemodynamic-immunotherapy
Multivariate covalent organic frameworks with tailored electrostatic potential promote nitrate electroreduction to ammonia in acid
Mussel-Inspired Polydopamine Composite Mesoporous Bioactive Glass Nanoparticles-An Exploration of Potential Metal-Ion Loading Platform and In Vitro Bioactivity
N-glycosylation-modifications-driven conformational dynamics attenuate substrate inhibition of d-lactonohydrolase
Nanoparticles insert a three dimensional cavity structure of proteins for function inhibition-The Case of CeO2 and SARS-CoV-2
NH3 production from absorbed NO with synergistic catalysis of Pd-C and functionalized ionic liquids
Non-fullerene electron acceptors constructed by four strong electron-withdrawing end groups
Non-Sacrificial Additive Enables a Non-Passivating Cathode Interface for 4.6 V Li LiCoO2 Batteries
Nonlinear relationship between heavy oil viscosity and asphaltene dispersion-A molecular dynamics simulation study
Novel ethylenediamine-β-cyclodextrin grafted membranes for the chiral separation of mandelic acid and its derivatives
Novel Strategy of Machine Learning for Predicting Henry’s Law Constants of CO2 in Ionic Liquids
Odorant-Binding Protein 6 Contributes High Binding Affinity to Insecticides in a Parasitic Wasp Meteorus pulchricornis (Hymenoptera-Braconidae)
One-Pot Asymmetric Synthesis of an Aminodiol Intermediate of Florfenicol Using Engineered Transketolase and Transaminase
One-step synthesis of Janus hydrogel via heterogeneous distribution of sodium α-linoleate driven by surfactant self-aggregation
Pathway of Oil-Soluble Additives to Reduce Heavy Crude Oil Viscosity Depends on the Molecular Characteristics of Asphaltene
Performance Evaluation and Molecular Dynamics Simulation in the Liquid-Liquid Extraction Process of Low Transition Temperature Mixture +n-Hexane+1,2-Dichloroethane
Phase behavior and extraction mechanism of methanol-n-hexane separation using choline-based deep eutectic solvent
Phospholipid Epitaxial Assembly Behavior on a Hydrophobic Highly Ordered Pyrolytic Graphite Surface
Photoelectron Spectroscopy and Computational Study on Microsolvated [B10H10]2– Clusters and Comparisons to Their [B12H12]2– Analogues
Physico-chemical properties of 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) diazonium ion-a theoretical investigation
Polymerization mechanism of polyferric aluminum phosphatic sulfate (PFAPS) and its flocculation effect on simulated dye wastewater
Probing the interaction mechanism of choline chloride-based deep eutectic solvents with flavonoid and polyphenol systems
Propeptide in Rhizopus chinensis Lipase-New Insights into Its Mechanism of Activity and Substrate Selectivity by Computational Design
Protein Matrix Control of Reaction Center Excitation in Photosystem II
PyConSolv-A Python Package for Conformer Generation of (Metal-Containing) Systems in Explicit Solvent
Quantitative Analysis of Physical Stability Mechanisms of Amorphous Solid Dispersions by Molecular Dynamic Simulation
Rational design of electrolytes operating at low temperatures-Does the co-solvent with a lower melting point correspond to better performance
Reconfiguration of intermolecular hydrogen bond for viscosity reduction of heavy oil
Regulated the aggregation of bile salts by β-Cyclodextrin and Tangeretin at the oil-water interface for inhibiting lipid digestion
How Different Substitution Positions of F, Cl Atoms in Benzene Ring of 5-Methylpyrimidine Pyridine Derivatives Affect the Inhibition Ability of EGFRL858RT790MC797S Inhibitors
A theoretical investigation of different point charges combined with GAFF and OPLS-AA for acetic anhydride
Study on simultaneous binding of resveratrol and curcumin to β-lactoglobulin-Multi-spectroscopic, molecular docking
High-χ Alternating Copolymers for Accessing Sub-5 nm Domains via Simulations
Interfacial Polarization and Electro-responsive Electrorheological Effect of Anionic and Cationic Poly(ionic liquid)s
Molecular Modeling on Morphology of 3,4-Bis(3-nitrofurazan-4-yl)furoxan Crystals in Dichloroethane or Benzene Mixture Solvents
Multisecond ligand dissociation dynamics from atomistic simulation
Poly(1,3,5-tris-(4-ethynylphenyl)-benzene) conjugated polymers as electrochemical sensors for hydrogen peroxide detection
Variation of Energy Transfer Rates across Protein-Water Contacts with Equilibrium Structural Fluctuations of a Homodimeric Hemoglobin
Revealing Binding and Unbinding Pathways of Small Molecules and Peptides to Enzymes with Enhanced Sampling Methods
Revealing the Two-Stage Charging Process in Sulfuric Acid Electrolyte by Molecular Dynamics Simulation
Robust Conductive Adhesives-A Strategy Using Metal-Doped Poly(ionic liquid)s
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Theoretical calculation on degradation mechanism of novel Copolyesters under CALB Enzyme
Thermal Decomposition Mechanism and Energy Release Law of Novel Cyclo-N5–-Based Nitrogen-Rich Energetic Salt
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Uni-ELF-A Multi-Level Representation Learning Framework for Electrolyte Formulation Design
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Water-Assisted Programmable Assembly of Flexible and Self-Standing Janus Membranes
Which is the main factor for improving the performance of the Graphene-MXene hybrid electrode
WS2@NC Square Hexahedral Nanosheets with Na+-DME-Solvent Cointercalation Mechanism for Fast and Durable Sodium Ion Storage
π-Electron-driven ionic liquids to enhance lithium recovery from spent batteries
π–π Interaction-Driven Charge Separation and Interlayer Transfer in Polymeric Carbon Nitride

作者
Author: KikuYoung 时间: 2025-8-6 10:35
感谢社长大大!

作者
Author: KikuYoung 时间: 2025-8-29 21:23

sobereva 发表于 2025-8-5 22:14
让他看Multiwfn手册3.9.16节，对RESP拟合过程交代得超级细致，默认设置下和RESP原文的流程完全一样

ante ...

Sober 老师好，我对 RESP 第二步限制中 =CH2 的等价限制有些疑问。
我去读了一下 Kollman, P. A. et al. A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: The RESP Model. J. Phys. Chem. 1993, 97 (40), 10269–10280. 原文。
相关的描述为「We suggest that sp2 and sp carbons should in general also be frozen in the second stage because their charges are likely to be much more well determined in the fit, in contrast to the more buried sp3 carbons. Also by implication, methylene groups should be treated like methyl groups, having their charges re-optimized in the second stage of the fit for the same reasons outlined above concerning forcing symmetry on the methyl hydrogen charges.」也就是原文推荐将 sp2 C 冻结。
而 Multiwfn 目前是在第二步对 =CH2 的 H 施加了等价限制的，我想知道此时 =CH2 是冻结 C 为上一步的电荷只优化 H，还是 C 也和 sp3 C 一样进行了新的拟合？=CH2 的拟合行为是和 antechamber 一样吗？论文原文和 Multiwfn 手册中的「methylene groups」让我有点不确定是指 -CH2- 还是 =CH2。
感谢 Sober 老师解惑～

作者
Author: sobereva 时间: 2025-8-30 05:26

KikuYoung 发表于 2025-8-29 21:23
Sober 老师好，我对 RESP 第二步限制中 =CH2 的等价限制有些疑问。
我去读了一下 Kollman, P. A. et al. ...

每一步拟合什么在Multiwfn输出信息里明确提示了

**** Stage 2: RESP fitting under strong hyperbolic penalty
Atom equivalence constraint imposed in this fitting stage:
Constraint 1: 2(H ) 3(H ) 4(H )
Constraint 2: 6(H ) 7(H )
Fitting objects: sp3 carbons, methyl carbons and hydrogens attached to them
Indices of these atoms:
1C 2H 3H 4H 5C 6H 7H

可见-CH2-和=CH2的碳不会在第二步重新拟合

作者
Author: KikuYoung 时间: 2025-8-30 08:29
本帖最后由 KikuYoung 于 2025-8-30 08:32 编辑

谢谢 sober 老师的解答！按我的理解，您的答复是想说第二步中等价限制不针对 C
我测试了一个包含 sp2 和所有 sp3 的分子，计算了 RESP 和 RESP 的第一步拟合电荷（即不加等价限制的 ESP）
发现体系中的 =CH2、-CH2-、-CH-（sp3）、-C-（sp3）等的 C 都应该在第二步进行了拟合，这也与 RESP 输出中列出的 fitting objects 的原子是一致的。

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**** Stage 2: RESP fitting under strong hyperbolic penalty
Atom equivalence constraint imposed in this fitting stage:
Constraint 1: 2(H ) 3(H )
Constraint 2: 11(H ) 12(H )
Constraint 3: 14(H ) 15(H ) 16(H )
Constraint 4: 18(H ) 19(H ) 20(H )
Fitting objects: sp3 carbons, methyl carbons and hydrogens attached to them
Indices of these atoms:
1C    2H    3H    6C 10C 11H 12H 13C 14H 15H
16H 17C 18H 19H 20H

Center Stage1-ESP    RESP
   1(C )  -0.3371585480  -0.3414429250
   2(H ) 0.1621109564 0.1556167260
   3(H ) 0.1507159430 0.1556167260
   4(C )  -0.2216553994  -0.2216553994
   5(H ) 0.1284125355 0.1284125355
   6(C ) 0.2760822201 0.2655041613
   7(C ) 0.3917777095 0.3917777095
   8(O )  -0.4098872069  -0.4098872069
   9(H )  -0.0368697238  -0.0368697238
10(C )  -0.0286636087  -0.0279003282
11(H ) 0.0310316642 0.0314766295
12(H ) 0.0259245459 0.0314766295
13(C )  -0.2314291835  -0.2210339729
14(H ) 0.0716869346 0.0591782090
15(H ) 0.0684125166 0.0591782090
16(H ) 0.0441762309 0.0591782090
17(C )  -0.4249567246  -0.4048835666
18(H ) 0.1113727023 0.1087524594
19(H ) 0.1172414081 0.1087524594
20(H ) 0.1116750276 0.1087524594

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