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:
http://www.wwpdb.org/docs.html
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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