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标题: 分子动力学模拟蛋白质三聚体能量无法最小化至生成gro文件 [打印本页]

作者
Author: mengdan1234 时间: 2025-4-9 22:19
标题: 分子动力学模拟蛋白质三聚体能量无法最小化至生成gro文件
本帖最后由 mengdan1234 于 2025-4-9 22:26 编辑

各位老师们好，
   学生在使用gromacs2020版，进行由ABC三种蛋白链组成的异三聚体结构的pdb文件做动力学模拟，来探究ABC三种蛋白间的相互作用。该蛋白质使用spdbv软件补齐了残缺残基结构，根据文献选择charm36力场,TIP3P水模型，十二面体水盒子。在准备阶段遇到蛋白质封端问题，如图 1，图2，图3，都没有报错，但是进行到能量最小化时，发现体系无法收敛，直接中断（图4），能力有限没有排查出来初始结构有什么问题，附件中放置了初始processed.gro和solv_ions.gro压缩文件。最后是top文件和能量最小化参数内容。
学生已经尝试分别更改ntegrator 为cg ;
            emtol  = 500.0 或者2000，
            nsteps  =10000  ；均不能生成em.gro,
            调整emstep  = 0.005时，得到em.gro,查看后蛋白结构断裂。
               实在不知哪个环节出现了问题。恳请各位大佬援助，学生感激不尽，非常感谢。

图1
(, 下载次数 Times of downloads: 6)

图2
(, 下载次数 Times of downloads: 6)

图3
(, 下载次数 Times of downloads: 6)

图4
(, 下载次数 Times of downloads: 5)

topol.top:
;       File 'topol.top' was generated
;       By user: Administrator (-1)
;       At date: Wed Apr  9 21:23:05 2025
;
;       This is a standalone topology file
;
;       Created by:
;                      :-) GROMACS - gmx pdb2gmx, 2020.6-MODIFIED (-:
;
;       Executable: D:\gmx2020.6\bin\\gmx.exe
;       Data prefix:  D:\gmx2020.6
;       Working dir:  D:\PRO\MD\ter
;       Command line:
;       gmx pdb2gmx -f 9cht(spdb).pdb -o processed.gro -ter
;       Force field was read from current directory or a relative path - path added.
;

; Include forcefield parameters
#include "./charmm36.ff/forcefield.itp"

; Include chain topologies
#include "topol_Protein_chain_A.itp"
#include "topol_Protein_chain_B.itp"
#include "topol_Protein_chain_C.itp"

; Include water topology
#include "./charmm36.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct    fcx       fcy       fcz
1 1    1000    1000    1000
#endif

; Include topology for ions
#include "./charmm36.ff/ions.itp"

[ system ]
; Name
UBIQUITIN-PROTEIN LIGASE E3A; 5 TRANSFERASE E3A,HUMAN PAPILLOMAVIRUS E6-ASSOCIATED PROTEIN,ONCOGENIC ; 6 PROTEIN-ASSOCIATED PROTEIN E6-AP,RENAL CARCINOMA ANTIGEN NY-REN-54;  ; IMMUNOGLOBULIN G-BINDING PROTEIN G/CELLULAR TUMOR ANTIGEN  ; 11 P53 FUSION PROTEIN; PROTEIN E6 in water

[ molecules ]
; Compound       #mols
Protein_chain_A    1
Protein_chain_B    1
Protein_chain_C    1
SOL       71509
NA             12

minim.mdp：
; minim.mdp - used as input into grompp to generate em.tpr
; Parameters describing what to do, when to stop and what to save
integrator  = steep       ; Algorithm (steep = steepest descent minimization)
emtol    = 1000.0       ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep    = 0.01       ; Minimization step size
nsteps    = 50000       ; Maximum number of (minimization) steps to perform

; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist       = 1       ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet ; Buffered neighbor searching
ns_type       = grid    ; Method to determine neighbor list (simple, grid)
coulombtype    = PME    ; Treatment of long range electrostatic interactions
rcoulomb       = 1.0    ; Short-range electrostatic cut-off
rvdw          = 1.0    ; Short-range Van der Waals cut-off
pbc          = xyz    ; Periodic Boundary Conditions in all 3 dimensions

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