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 <[email protected]> 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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