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

[Justin A. Lemkul]

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 
documentation:

http://ffamber.cnsm.csulb.edu/#usage

-Justin

> 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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================