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

Oliver Grant olymacfoogal at gmail.com
Tue Jul 6 12:58:24 CEST 2010

Hi Abdul,

Could you post your pdb and your command line please? I'll take a look for
you. I think this is a bugzilla as mark suggested but maybe more
specifically an amber ports problem.


On 6 July 2010 09:48, abdul wadood <wadoodbiochemist at hotmail.com> 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
> 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.
> Your help in this respect will by highly appreciated.
> Thanks in advance
> many regards
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