[gmx-users] (no subject)

SLN Prasad Reddy sreeyapu at rediffmail.com
Thu Aug 12 18:05:44 CEST 2004

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  Hello gromacs users,
             I am simulating a protien with ATP.  Gromacs did accept protein part of pdb file where as it did not accept ATP.I was told by a gromacs user to change the atom names as per *.rtp ( Since i used force field 0 of version 3.1.1 or force field 4 of version 3.2, the corrosponding one is ffgmx.rtp) file. But ATP of ffgmx.rtp contains hydrogens which are not there in pdb file. Hence i protonated atp and used. If i use grompp command to create *.tpr file it is complaining dihedral angle problem especially with ATP atoms.Any suugestions to over come this problem is deeply appreciated. 

Thanking you


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