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
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