目的：
批量生成小分子拓扑文件，以便用于gmx动力学模拟
安装：
安装acpype
option 1：pip install acpype
option 2:conda install -c acpype acpype
安装ambertools20
官网：
http://ambermd.org/AmberTools.php
option 1:直接官网下载安装
option 2:conda install -c conda-forge ambertools
使用：
In ：
代码语言：javascript复制acpype -helpOut：
代码语言：javascript复制usage:
acpype -i _file_ [-c _string_] [-n _int_] [-m _int_] [-a _string_] [-f] etc. or
acpype -p _prmtop_ -x _inpcrd_ [-d]
output: assuming 'root' is the basename of either the top input file,
the 3-letter residue name or user defined (-b option)
root_bcc_gaff.mol2: final mol2 file with 'bcc' charges and 'gaff' atom type
root_AC.inpcrd : coord file for AMBER
root_AC.prmtop : topology and parameter file for AMBER
root_AC.lib : residue library file for AMBER
root_AC.frcmod : modified force field parameters
root_GMX.gro : coord file for GROMACS
root_GMX.top : topology file for GROMACS
root_GMX.itp : molecule unit topology and parameter file for GROMACS
root_GMX_OPLS.itp : OPLS/AA mol unit topol & par file for GROMACS (experimental!)
em.mdp, md.mdp : run parameters file for GROMACS
root_NEW.pdb : final pdb file generated by ACPYPE
root_CNS.top : topology file for CNS/XPLOR
root_CNS.par : parameter file for CNS/XPLOR
root_CNS.inp : run parameters file for CNS/XPLOR
root_CHARMM.rtf : topology file for CHARMM
root_CHARMM.prm : parameter file for CHARMM
root_CHARMM.inp : run parameters file for CHARMM
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
input file name with either extension '.pdb', '.mdl'
or '.mol2' (mandatory if -p and -x not set)
-b BASENAME, --basename BASENAME
a basename for the project (folder and output files)
-x INPCRD, --inpcrd INPCRD
amber inpcrd file name (always used with -p)
-p PRMTOP, --prmtop PRMTOP
amber prmtop file name (always used with -x)
-c {gas,bcc,user}, --charge_method {gas,bcc,user}
charge method: gas, bcc (default), user (user's
charges in mol2 file)
-n NET_CHARGE, --net_charge NET_CHARGE
net molecular charge (int), for gas default is 0
-m MULTIPLICITY, --multiplicity MULTIPLICITY
multiplicity (2S 1), default is 1
-a {gaff,amber,gaff2,amber2}, --atom_type {gaff,amber,gaff2,amber2}
atom type, can be gaff, gaff2, amber (AMBER14SB) or
amber2 (AMBER14SB GAFF2), default is gaff
-q {mopac,sqm,divcon}, --qprog {mopac,sqm,divcon}
am1-bcc flag, sqm (default), divcon, mopac
-k KEYWORD, --keyword KEYWORD
mopac or sqm keyword, inside quotes
-f, --force force topologies recalculation anew
-d, --debug for debugging purposes, keep any temporary file
created
-o {all,gmx,cns,charmm}, --outtop {all,gmx,cns,charmm}
output topologies: all (default), gmx, cns or charmm
-z, --gmx4 write RB dihedrals old GMX 4.0
-t, --cnstop write CNS topology with allhdg-like parameters
(experimental)
-e {tleap,sleap}, --engine {tleap,sleap}
engine: tleap (default) or sleap (not fully matured)
-s MAX_TIME, --max_time MAX_TIME
max time (in sec) tolerance for sqm/mopac, default is
10 hours
-y, --ipython start iPython interpreter
-w, --verboseless print nothing
-g, --disambiguate disambiguate lower and uppercase atomtypes in GMX top
file
-u, --direct for 'amb2gmx' mode, does a direct conversion, for any
solvent
-l, --sorted sort atoms for GMX ordering
-j, --chiral create improper dihedral parameters for chiral atoms
in CNS
In：
代码语言：javascript复制#默认电荷是bcc，默认力场为gaff
#输入test.pdb文件，输出符号标志符表示为sqm，输出类型为gmx相关
acpype -i test.pdb -b sqm -o gmxOut：
代码语言：javascript复制#输出文件名以及类型如下
em.mdp md.mdp sqm_AC.inpcrd sqm_AC.prmtop sqm_GMX.gro sqm_GMX_OPLS.itp sqm_GMX.top sqm.mol2 sqm.pdb
leap.log sqm_AC.frcmod sqm_AC.lib sqm_bcc_gaff.mol2 sqm_GMX.itp sqm_GMX_OPLS.top sqm.in sqm.out sqm.pkl可以进行加入gmx进行md模拟
