[gmx-users] protein/dmso simulation

Justin A. Lemkul jalemkul at vt.edu
Mon Aug 18 21:08:53 CEST 2008

prasun kumar wrote:
> dear users
> I am trying to run the simulation fo a protein/DMSO system,Its working 
> well till genbox but while running GROMPP I am gettin a fatal 
> error,which is
> atom type 'SD' not found.
> SD is given in the gro & itp file of DMSO.
> what should I do to overcome this problem........
> I have tried by replacing SD by S,but its of no use
> I should generate a separate top file for DMSO  and then include it in 
> the topology file generated for protein
> I tried to do this also using PDB2GMX command  but again I am gettin 
> error related to 'SD'

Which force field are you using?  If you look at the .rtp entry (if present), it 
will tell you the correct atomic nomenclature.  Otherwise, you have an 
inconsistency in the atomtypes definition in your topology.


> please help me..........
> regards &thanx in advance
> -- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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