[gmx-users] CHARMM to GROMACS conversion and inclusion of bonded, non-standard residues and parameters

Justin Lemkul jalemkul at vt.edu
Wed Jul 9 14:18:14 CEST 2014

On 7/9/14, 8:11 AM, Nikolaos Michelarakis wrote:
> Hello again,
> This what I have been trying to do so far. This is the command to run the
> script:
> ./cgenff_charmm2gmx.py PTC 2e7z-ptc.mol2 2e7z-ptc.str charmm36-mar2014.ff
> and this is the error I have been getting along with 2 Notes:
> 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  charmm36-mar2014.ff/forcefield.doc : 2b8
> NOTE3: 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. top
> 96 142
> The file names I am using are:
>   2e7z-ptc.str          charmm36-mar2014.ff
> 2e7z-ptc.mol2  cgenff_charmm2gmx.py
> These are the contents of the .mol2 and .str files respectively:
> https://drive.google.com/file/d/0BzqRbRx4Ynf0TUg3blBOTmV0Qzg/edit?usp=sharing
> (mol2)
> https://drive.google.com/file/d/0BzqRbRx4Ynf0VThMSnNYMU1XVmM/edit?usp=sharing
> (str)

There's a mismatch between the structures.  Your coordinates (mol2) have 96 
atoms, but the topology has 142.  The problem comes from the fact that your mol2 
file has no H atoms.



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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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


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