[gmx-users] cgenff script failed

[Justin Lemkul]

On 1/18/16 2:32 PM, Albert wrote:
> Dear:
>
> I've trying to use the following command to generate ligand toplogy for Gromacs:
>
> cgenff_charmm2gmx.py UNK ligand.mol2 ligand.str ./charmm36.ff
>
> but it failed with messages:
>
> error in atomgroup.py: read_mol_coor_only: natoms in mol2 .ne. top
> 54 0
>
> It is really strange to see this error since it claimed that there is 0 atom in
> my .top file.... I obtained the ligand.str file from paramchem website without
> any warnings or errors.
>

This probably means your residue isn't named "UNK" in the stream file.

-Justin

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

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