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

[Oliver Grant]

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.

Oliver

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
>
> ------------------------------
> Hotmail has tools for the New Busy. Search, chat and e-mail from your
> inbox. Learn more.<http://www.windowslive.com/campaign/thenewbusy?ocid=PID28326::T:WLMTAGL:ON:WL:en-US:WM_HMP:042010_1>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100706/3c80910b/attachment.html>