[gmx-users] CGenFF generated prm/itp overriding and messing with charmm36-nov2016.ff?

Justin Lemkul jalemkul at vt.edu
Mon Mar 13 01:58:08 CET 2017

On 3/12/17 8:21 PM, Jonathan Saboury wrote:
> Sorry for the delay, I didn't see this email.
> I don't believe it is a problem with gromacs, but a problem with
> cgenff_charmm2gmx.py from (from
> http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/cgenff_charmm2gmx.py
> )
> cgenff_charmm2gmx.py wrote the .pdb atom names from columns 14-17 instead
> of 13-16. This code works fine if the atom names in .str outputted by
> https://cgenff.paramchem.org/initguess/ is <=3 chars long. If it is 4 chars
> long (one char in the atom name will be in column 17, which isn't read by
> gromacs, and it shouldn't) the gromacs errs because the gmx outputed pdbs
> (from editconf, solvate, the the like)  does not match the atom name in
> .top.
> I have contacted them about this error.

I fixed the script.  Please get the new version from our website.

Note that the CGenFF server still produces old (version 3.0.1) topologies and is 
therefore not compatible with our C36/CGenFF 4.0 force field files.  We're 
working on getting that updated but there are technical issues holding things back.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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