[gmx-users] protein/dmso simulation

[Bhanu]

Try "genbox -cp *.gro -ci dmso.gro -p *.top -o *.gro"
Gro file for dmso comes built-in with gromacs 3.3. As Justin has directed,
forcefields do matter.


On 19/08/2008, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
>
> 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
>>
>> --
>> PRASUN (ASHOKA)
>>
>>
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>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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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