[gmx-users] Error in creating parameter files using SwissParam

[Dallas Warren]

This is nothing to do with the GROMACS software, you should be asking
http://www.swissparam.ch/

The error seems to be self explanatory, did you check your mol2 file?
http://www.swissparam.ch/SwissParam_mol2_file.html

I would suggest loading the mol2 file you have using pymol or vmd, and
check to ensure it as it should be.

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

On Mon, 1 Jul 2019 at 17:26, GAYATHRI S <gayathri.s at iitb.ac.in> wrote:
>
> Dear GROMACS users and developers,
>
> I want to run MD simulation of a protein bound to FAD using CHARMM36 force
> field. However, I need to generate the parameter files of FAD first.
> Hence, I followed the following steps:
>
> 1.      Downloaded the .pdb structure file from RCSB PDB databank
> 2.      Kept the coordinates of FAD and deleted the rest
> 3.      Added H-atoms and converted to .mol2 file using UCSF Chimera (as
> suggested in the website)
> 4.      Submitted this file as input in the SwissParam site
>
> Error obtained
>
> Thank you for using SwissParam.
>
> Unfortunately, topology and parameters were not successfully generated for
> 3w2g_fad.
> A failure report can be found below.
>
> Failure report:
>
> Possible problem with molecular topology in 3w2g_fad.mol2.
> SwissParam will try to reconstruct the topology from coordinates only.
>
>
> Topology and parameters were NOT generated. Please check the validity of
> your molecule.
> - Are all hydrogens present in the mol2 file?
> - Is the mol2 file correct? Please, read "How to obtain a correct mol2
> file?" in the www.swissparam.ch website.
>
> Kindly suggest how I can resolve the issue.
>
> Thank you.
>
> Regards,
> Gayathri S
>
>
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