[gmx-users] RE: gmx-users Digest, Vol 75, Issue 23

Justin A. Lemkul jalemkul at vt.edu
Tue Jul 6 12:52:18 CEST 2010

abdul wadood wrote:
> Dear gmx-usrs
> Thanks you all for you valuable suggestion. Unfortunately, the problem 
> is still exist.
> I add the hydrogen to LEU2 but then the error come for the next amino acid.
> I also used the -ignh but the error was same.
> I dont understand one thing which is that when I used simply Pro instead 
> of NPRO which is N ternimal amino acid and SER instead of CSER which is 
> C-terminal amino acid in my protein. Then no error come and pdb2gmx 
> produced top file and other file without any error. However, the message 
> come that
> N-terminus: none
> C-terminus: none

This is a normal message from pdb2gmx, since there are no termini options for 
the Amber force fields; they work differently from the others.  I wouldn't use 
this .top/.gro combination, however, as the N- and C-termini likely don't 
correspond to anything meaningful.  Look at the .gro and .top and you will 
hopefully see what I mean.

> I am using gromacs 4.0.5
> Now, I am in doubt that I am going in the right way or I have to modify 
> PRO with NPRO and SER with CSER.

The Amber ports (and Amber force fields, in general) require proper 
nomenclature, so yes, you should be using NPRO and CSER.  Please consult the 



> Your help in this respect will by highly appreciated.
> Thanks in advance
> many regards
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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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