[gmx-users] polymer-protein

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 15 17:28:25 CET 2010

P.R.Anand Narayanan wrote:
> Dear Gromacs users,
> I have to attach a chemical polymer to a protein and when I created 
> peptide bonds and saved it, the entire format of the pdb file changed. 
> That is the entire identity of the protein was lost and the pdb file was 
> saved in the form of ATOMS and not residues.

You'll have to give some example of what you mean.  Otherwise, we're left to 
assume that you improperly generated the coordinate file, but you haven't even 
mentioned how you've done what you're attempting.

> Are there any solutions to this or can I Use the same in gromacs??????? 
> If yes, how can I use it in the pdb2gmx command????

You cannot use pdb2gmx unless you have the appropriate .rtp entries (and perhaps 
specbond.dat entries) defined.  See the numerous discussions in the list archive 
as well as pdb2gmx usage information and errors (and how to deal with them) on 
the Gromacs site.


> Please help,
> Thanking you,
> regards,
> Anand
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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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