[gmx-users] Generate the Topology with CGenFF :: Error message

[Justin Lemkul]

On 2/3/20 9:06 AM, Adarsh V. K. wrote:
> Dear all,
> At present the ProDrg server is not functioning properly in generating
> ligand topology files. How to generate topology files using ProDrg
> While try to Generate the topology with CGenFF server, it returns following
> Error message
> How to manage this problem?
> --------------------------------------------------------------
> NOTE 1: Code tested with python 2.7.12. Your version: 2.7.15+ (default, Oct
>   7 2019, 17:39:04) [GCC 7.4.0]
>
> NOTE 2: Please be sure to use the same version of CGenFF in your
> simulations that was used during parameter generation:
> --Version of CGenFF detected in  1MD19DB00931.str : 3.0.1
> --Version of CGenFF detected in  charmm36-mar2019.ff/forcefield.doc : 4.1
>
> WARNING: CGenFF versions are not equivalent!
>
> NOTE 3: 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: no. of atoms in mol2 (54) and
> top (0) are unequal
> Usually this means the specified residue name does not match between str
> and mol2 files
> -----------------------------------------------------------

The last line of the note tells you the problem. Correct the residue 
name in the stream file.

-Justin

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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
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Virginia Tech Department of Biochemistry
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jalemkul at vt.edu | (540) 231-3129
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