Hi Justin, Thank you for your answer. It made me to think again and I found the source of the problem (silly mistake). Thanks again!
Seunghwan Lee --- On Fri, 10/16/09, Justin A. Lemkul <jalem...@vt.edu> wrote: > From: Justin A. Lemkul <jalem...@vt.edu> > Subject: Re: [gmx-users] Lipid-protein tuturial by Lemkul > To: "Discussion list for GROMACS users" <gmx-users@gromacs.org> > Date: Friday, October 16, 2009, 11:45 AM > > > seunghwan lee wrote: > > Hi > > > > I am new to Gromacs and going through some tutorials. > I am working on lipid-protein tutorial given by Justin > Lemkul and I am stuck with the very first step. When I > execute pdb2gmx to generate .top file and .pdb without > hydrogen, > > > > pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro > -ignh -ter -water spc > > > > I got the following message: > > > > > ------------------------------------------------------- > > Program pdb2gmx, VERSION 4.0.4 > > Source code file: pgutil.c, line: 87 > > > > Fatal error: > > Atom H not found in residue 17 while adding improper > > > > > ------------------------------------------------------- > > > > I made the correction to ffG53a6.rtp file as suggested > by Justin, but apparently I am still having a problem with > -NH2 residue (#17). Is there any other corrections I need to > do in order to make this work? > > > > No other correction is necessary. If you fixed the > .rtp file correctly, you should not have any problems. > > -Justin > > > Thanks for your help!! > > Seunghwan Lee > > > > > > > _______________________________________________ > > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > > -- ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@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-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
