[gmx-users] Re: protein/dmso simulation

Vitaly Chaban chaban at univer.kharkov.ua
Tue Aug 19 10:14:38 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.
> -Justin
>> please help me..........
>> regards &thanx in advance

If you are using DMSO preequilibrated coordinates provided with
gromacs as I guess there's dmso.itp file in the same folder. Just
include dmso.itp in your topol.top. This will add the lacking

Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq., 4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua
skype: vvchaban

More information about the gromacs.org_gmx-users mailing list