[gmx-users] problem with generation of .gro file

[Justin A. Lemkul]

subarna thakur wrote:
> Hello,
> I am running the pdb2gmx command for a homodimer protein with SF4 (a 
> ferro-sulphur cluster) ligand but it fails to generate the .gro file. A 
> error is coming SF4 not found in residue topology database. I have 
> trired all the different force fields. Can anybody please tell me how to 
> correct the error? How to modify the rtp file to consider the ligand? 
>  

Dealing with the error:

http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_residue_topology_database

The unfortunate news that you have your work cut out for you:

http://wiki.gromacs.org/index.php/Parameterization
http://wiki.gromacs.org/index.php/Exotic_Species

Parameterization is an advanced topic, especially when dealing with strange 
species like an iron-sulfur cluster.  Read the "exotic species" article closely.

-Justin

> Subarna thakur
> University of north bengal
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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