[gmx-users] Gromacs tutorial

[Justin Lemkul]

On 10/11/19 8:49 AM, Suprim Tha wrote:
> I was trying gromacs tutorial on molecular dynamics simulation of
> protein-ligand complex. Everything was going well until the step to
> convert CHARMM
> jz4.str file into GROMACS files using the command
> python cgenff_charmm2gmx_py2.py JZ4 jz4.mol2 jz4.str charmm36-mar2019.ff
> The error was:
> Error in atomgroup.py: read_mol2_coor_only: no. of atoms in mol2 (22) and
> top (0) are unequal
> Usually this means the specified residue name does not match between str
> and mol2 files.
> I have attached the generated str and mol2 files.

The mailing list does not accept attachments. Make sure the residue name 
in the .str file matches the .mol2 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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