Thank you very much, I will have a look.
Hi @alanwilter, can I ask do you have a detailed explanation for the possible values that can follow the various options?
acpype -i _file_ [-c _string_] [-n _int_] [-m _int_] [-a _string_] [-f]
acpype -p _prmtop_ -x _inpcrd_ [-d]
For example, I guess -c is charge method, -n is net charge. But could you please provide a table like this? Thank you!
Sorry @lanselibai but was acpype -h not enough?
usage:
acpype -i _file_ | _SMILES_string_ [-c _string_] [-n _int_] [-m _int_] [-a _string_] [-f] etc. or
acpype -p _prmtop_ -x _inpcrd_ [-d | -w]
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 type like '.pdb', '.mdl', '.mol2' or SMILES string (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 (default), amber (AMBER14SB) or amber2 (AMBER14SB + GAFF2)
-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 (not allowed with arg -w)
-w, --verboseless print nothing (not allowed with arg -d)
-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)
-s MAX_TIME, --max_time MAX_TIME
max time (in sec) tolerance for sqm/mopac, default is 3 hours
-y, --ipython start iPython interpreter
-g, --merge Merge lower and uppercase atomtypes in GMX top file if identical parameters
-u, --direct for 'amb2gmx' mode, does a direct conversion, for any solvent (EXPERIMENTAL)
-l, --sorted sort atoms for GMX ordering
-j, --chiral create improper dihedral parameters for chiral atoms in CNS
-v, --version Show the Acpype version and exit
@alanwilter I see. Sorry I missed the later part. Yes, acpype.py -h is enough.
By the way, can I ask, is that possible for acpype.py to repair the bond? I download the PDB/SDF from pdb ligand website. But it incorrectly labels the S=O double-bond as S-O single bond. The acpype.py processes the PDB, and generates the mol2 file, which still keeps the S-O single bond.
I tried xtb, still could not repair the bond.
Hi @alanwilter, can I ask is that possible to set -n auto to guess the net charge in the offline acpype? The online webserver has this function, but the offline one does not have it.
You can try to use SMILES as an input. Double or single bond will change the protonation of atoms involved or the total charge of your system. You need to know what your want and then what you’re doing.
Haven’t you ever read the log or the stdout when running acpype?
acpype -i AAA.pdb
==========================================================================
| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.1.4 (c) 2022 AWSdS |
==========================================================================
WARNING: no charge value given, trying to guess one...
==> ... charge set to 0
...
Anyway, I will add something about it to the help to emphasize that acpype already has the auto charge.
thank you very much, by not supplying the charge for it to guess is a good idea.
Hi @lanselibai
I have almost the same problem can you help me please?