[gmx-users] Re: protein/dmso simulation

[Vitaly Chaban]

> 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
definitions.

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