Pdb2gmx

1 介绍

This program reads a pdb file, reads some database files, adds hydrogens to the molecules and generates coordinates in Gromacs (Gromos) format and a topology in Gromacs format. These files can subsequently be processed to generate a run input file.

pdb2gmx 读取 pdb 文件，读取数据文件并给分子加氢，同时生成 Gromacs 文件格式(.gro)和一个拓扑文件

The force fields in the distribution are currently:

• oplsaa OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
• G43b1 GROMOS96 43b1 Vacuum Forcefield
• G43a1 GROMOS96 43a1 Forcefield
• G43a2 GROMOS96 43a2 Forcefield (improved alkane dihedrals)
• G45a3 GROMOS96 45a3 Forcefield
• G53a5 GROMOS96 53a5 Forcefield
• G53a6 GROMOS96 53a6 Forcefield
• gmx Gromacs Forcefield (a modified GROMOS87, see manual)
• encads Encad all-atom force field, using scaled-down vacuum charges
• encadv Encad all-atom force field, using full solvent charges

The corresponding data files can be found in the library directory with names like ffXXXX.YYY. Check chapter 5 of the manual for more information about file formats. By default the forcefield selection is interactive, but you can use the -ff option to specify one of the short names above on the command line instead. In that case pdb2gmx just looks for the corresponding file.

Note that a pdb file is nothing more than a file format, and it need not necessarily contain a protein structure. Every kind of molecule for which there is support in the database can be converted. If there is no support in the database, you can add it yourself.

The program has limited intelligence, it reads a number of database files, that allow it to make special bonds (Cys-Cys, Heme-His, etc.), if necessary this can be done manually. The program can prompt the user to select which kind of LYS, ASP, GLU, CYS or HIS residue she wants. For LYS the choice is between LYS (two protons on NZ) or LYSH (three protons, default), for ASP and GLU unprotonated (default) or protonated, for HIS the proton can be either on ND1 (HISA), on NE2 (HISB) or on both (HISH). By default these selections are done automatically. For His, this is based on an optimal hydrogen bonding conformation. Hydrogen bonds are defined based on a simple geometric criterium, specified by the maximum hydrogen-donor-acceptor angle and donor-acceptor distance, which are set by -angle and -dist respectively.

Option -merge will ask if you want to merge consecutive chains into one molecule definition, this can be useful for connecting chains with a disulfide brigde or intermolecular distance restraints.

pdb2gmx will also check the occupancy field of the pdb file. If any of the occupanccies are not one, indicating that the atom is not resolved well in the structure, a warning message is issued. When a pdb file does not originate from an X-Ray structure determination all occupancy fields may be zero. Either way, it is up to the user to verify the correctness of the input data (read the article!).

During processing the atoms will be reordered according to Gromacs conventions. With -n an index file can be generated that contains one group reordered in the same way. This allows you to convert a Gromos trajectory and coordinate file to Gromos. There is one limitation: reordering is done after the hydrogens are stripped from the input and before new hydrogens are added. This means that you should not use -ignh.

The .gro and .g96 file formats do not support chain identifiers. Therefore it is useful to enter a pdb file name at the -o option when you want to convert a multichain pdb file.

The option -vsite removes hydrogen and fast improper dihedral motions. Angular and out-of-plane motions can be removed by changing hydrogens into virtual sites and fixing angles, which fixes their position relative to neighboring atoms. Additionally, all atoms in the aromatic rings of the standard amino acids (i.e. PHE, TRP, TYR and HIS) can be converted into virtual sites, elminating the fast improper dihedral fluctuations in these rings. Note that in this case all other hydrogen atoms are also converted to virtual sites. The mass of all atoms that are converted into virtual sites, is added to the heavy atoms.

Also slowing down of dihedral motion can be done with -heavyh done by increasing the hydrogen-mass by a factor of 4. This is also done for water hydrogens to slow down the rotational motion of water. The increase in mass of the hydrogens is subtracted from the bonded (heavy) atom so that the total mass of the system remains the same.

2 文件

option	filename	type	description
-f	eiwit.pdb	Input	Structure file: gro g96 pdb tpr tpb tpa. 读入gro g96 pdb tpr tpb tpa文件。
-o	conf.gro	Output	Structure file: gro g96 pdb. 指定一个新生成的gro g96 pdb文件
-p	topol.top	Output	Topology file. 指定新产生的拓扑文件(.top)，拓扑结构包含了所有的力场参数。
-i	posre.itp	Output	Include file for topology
-n	clean.ndx	Output, Opt.	Index file
-q	clean.pdb	Output, Opt.	Structure file: gro g96 pdb

3 其他选项

option	type	default	description
-[no]h	bool	no	Print help info and quit
-nice	int	0	Set the nicelevel
-[no]merge	bool	no	Merge chains into one molecule definition
-ff	string	select	Force field, interactive by default. Use -h for information. 用来指定力场。
-water	enum	spc	Water model to use: with GROMOS we recommend SPC, with OPLS, TIP4P: spc, spce, tip3p, tip4p, tip5p or f3c. 指定水模型。
-[no]inter	bool	no	Set the next 8 options to interactive
-[no]ss	bool	no	Interactive SS bridge selection
-[no]ter	bool	no	Interactive termini selection, iso charged. 设定肽链末端的情况
-[no]lys	bool	no	Interactive Lysine selection, iso charged
-[no]arg	bool	no	Interactive Arganine selection, iso charged
-[no]asp	bool	no	Interactive Aspartic Acid selection, iso charged
-[no]glu	bool	no	Interactive Glutamic Acid selection, iso charged
-[no]gln	bool	no	Interactive Glutamine selection, iso neutral
-[no]his	bool	no	Interactive Histidine selection, iso checking H-bonds.单个指定HIS残基的质子化位置。
-angle	real	135	Minimum hydrogen-donor-acceptor angle for a H-bond (degrees)
-dist	real	0.3	Maximum donor-acceptor distance for a H-bond (nm)
-[no]una	bool	no	Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine
-[no]ignh	bool	no	Ignore hydrogen atoms that are in the pdb file. 忽略文件中的氢原子
-[no]missing	bool	no	Continue when atoms are missing, dangerous
-[no]v	bool	no	Be slightly more verbose in messages
-posrefc	real	1000	Force constant for position restraints
-vsite	enum	none	Convert atoms to virtual sites: none, hydrogens or aromatics
-[no]heavyh	bool	no	Make hydrogen atoms heavy
-[no]deuterate	bool	no	Change the mass of hydrogens to 2 amu

4 参见

• Gromacs Manual
• wangwei. Gromacs学习的基础知识. [EB/OL]. [2011-03-31]. http://www.mdbbs.org/thread-23170-1-1.html.