[gmx-users] protein/dmso simulation

prasun kumar prasun30 at gmail.com
Mon Aug 18 19:53:08 CEST 2008

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'
please help me..........
regards &thanx in advance

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