[gmx-users] cgenff_charmm2gmx conversion error

Justin Lemkul jalemkul at vt.edu
Thu Dec 31 15:01:37 CET 2015

On 12/31/15 1:54 AM, Nikhil Maroli wrote:
> Dear all,
> im trying to make itp file using cgenff_charmm2gmx.py i have given these
> comment
>   python cgenff_charmm2gmx.py LIG ligand.mol2 ligand.str charmm36-jun2015.ff
> i got following error
> *NOTE2: Please be sure to use the same version of CGenFF in your
> simulations that was used during parameter generation:--Version of CGenFF
> detected in  ligand.str : 3.0.1--Version of CGenFF detected in
> charmm36-jun2015.ff/forcefield.doc : 3.0.1NOTE3: In order to avoid
> duplicated parameters, do NOT select the 'Include parameters that are
> already in CGenFF' option when uploading a molecule into CGenFF.error in
> atomgroup.py: read_mol2_coor_only: natoms in mol2 .ne. top33 0*
> i have checked the number of atoms in both mol2 and str file both are
> same,33 number

Your residue is not named "LIG" in the ligand.str file:

RESI molecu

Rename it and the script will work.



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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