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标题: charmm36-jul2022 力场中可选择的蛋白C端/N端及核酸5'/3'-ter 列表 (英文) [打印本页]

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Author: student0618 时间: 2024-6-26 20:42
标题: charmm36-jul2022 力场中可选择的蛋白C端/N端及核酸5'/3'-ter 列表 (英文)
本帖最后由 student0618 于 2024-6-26 20:41 编辑

charmm36-jul2022 力场中可选择的蛋白C端/N端及核酸5'/3'-ter 列表

(Types of protein/nucleic acid terminus in the charmm36-jul2022 forcefiled for gromacs)

(If anyone has a Chinese translation of these terminus types, feel free to provide in reply. I'll add to this post with acknowledgement to help others who use "full-text search" of Chinese terms in this forum. I can read and write in Chinese, but I'm not confident in the translation of technical terms. Also, please let me know for any comments or issues.)

This is a quick reference of protein/nucleic acid termini in CHARMM36 forcefield available in the "charmm36-jul2022.ff" port for gromacs. For details of how gmx handled terminal patching, please refer to the following forum post: http://bbs.keinsci.com/thread-40001-1-1.html

A. Procedures of using the terminal patches

1. Download forcefield files in gmx format

The latest version of CHARMM36 forcefield for GROMACS can be obtained from https://mackerell.umaryland.edu/charmm_ff.shtml#gromacs
After you download the file, extract it to your working directory.

2a. Preparation: nucleic acids (DNA/RNA)

For DNA/RNA, first you should follow instructions in the following post (http://bbs.keinsci.com/thread-34465-1-1.html). I provide a rough English translation here (using the updated FF version): From the "charmm27.ff" directory bundled with Gromacs, copy the "dna.arn" file to the "charmm36-jul2022.ff" directory and rename it to "na.arn"
Alternatively, you may edit your pdb file to replace OP1/OP2 with O1P/O2P e.g. using sed or a text editor.

2b. Preparation: for acetylated N-terminus (ACE) and N-methylamide C-terminus (NME) in protein

For the ACE and NME caps, they are defined as another residue like in Amber. Build these caps as an additional residue, e.g. with PyMOL builder, before you process it with pdb2gmx.

3. Running pdb2gmx with interactive termini selection

Termini for protein and nucleic acids (except ACE and NME) can be selected if you add a -ter flag when you run pdb2gmx, e.g.

gmx pdb2gmx -f system.pdb -o system_processed.gro -p topol.top -ter -ignh

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Once it prompt to let you choose the terminus type, select the the one you would like to use. Refer to Section B for the full name of each terminus type in the list.

For ACE and NME caps in protein, choose "None" when prompted for terminal selection.

B. Summary of the terminus type supported (forcefield version July 2022)

Here is a list of terminus type and the full name of the terminal, information extracted from tdb and rtp files. I use text instead of figure for easier full-text search. For the detailed atom typing and topologies, please refer to the corresponding files.

1. Protein 蛋白
1a. N-terminal N端

NH3+ = standard N-terminus
NH2 = neutral N-terminus
None = do-nothing terminus
**ACE = acetylated N-terminus (**defined as a separeate residue, not selected from -ter. Build it before you use pdb2gmx and choose "None".)

1b. C-terminal C端

COO- = standard C-terminus
COOH = protonated C-terminus
CT2 = amidated C-terminus
CT1 = methylated C-terminus
None = do-nothing terminus
**NME = N-methylamide C-terminus (**defined as a separeate residue, not selected from -ter. Build it before you use pdb2gmx and choose "None".)

2. DNA/RNA 核酸
2a. 5'-terminal

5TER = 5'-terminal hydroxyl
5MET =5'-ribose methyl
5PHO = 5'-terminal phosphate (*5PHO is protonated)
5POM = 5'-terminal Methyl-Phosphate
None = do-nothing terminus

2b. 3'-terminal

3TER = 3'-terminal hydroxyl
None = do-nothing terminus

C. Remarks and related notes

CHARMM-GUI support more terminus types including the 3'-phosphate in nucleic acids. I skip the details here since the server is rather straightforward to use.
CHARMM forcefield use terminal patching and treat a terminal patching as the same residue, except for ACE and NME caps. While in Amber forcefield, most of them are defined as another residue. To do something equivalent in Amber, consult related documents e.g. Amber manual or aminoacid.rtp files.

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