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

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 2 13:58:32 CEST 2009

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:


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


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


> 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


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