[gmx-users] pdb file badly broken after changing residue name a/c to amber.rtp file

nitu sharma sharmanitu35 at gmail.com
Sat Jul 4 08:36:50 CEST 2009

Dear justin

                      I am trying to do simulation of dna-protein complex  .
For this I am using amber port with gromacs-4.0.3  but for this a/c to
ffamber.rtp file entry i hqve to make changes in my  .pdb file residues like
the DNA base name in this is only A ,C ,G,T so a/c to amber.rtp file entry
I have converted it in DA,DC,DG,DT but when i have changed the name and atom
name also my pdb file badly broken. Becoz after that when I have seen it in
pymol viewer the structure was totally crashed .
so , I want to ask you how can I get rid from this problem for doing
simulation of dna-protein complexusing amber port with gromacs?

so please suggest me proper methodology to make my pdb file stable even
after changing residue name a/c to amber .rtp entry.

Nitu harma.
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