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

Justin A. Lemkul jalemkul at vt.edu
Sat Jul 4 11:36:52 CEST 2009

nitu sharma wrote:
> 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?

You probably changed the spacing when you changed the residue names.  PDB files 
are fixed-format, according to these guidelines:



> 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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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