Quoting OZGE ENGIN <[EMAIL PROTECTED]>: > Ok, it should be better to describe the problem in a more detailed way. > I got this structure from Swiss-modeler program. I do not think I have a > problem with the starting structure because I truncated the protein at some > PRO residue, and got no error at all. So, there is something wrong about the > nomenclature of the N terminus. I read things in the link, searched the web > and made some discussion with my friend, but I could not find the source of > the error :)
So have I got it correct that you truncated the N-terminus originally, and are now adding residues back? It still suggests to me that you've generated a poor starting structure; the nomenclature should not be causing the issue. Identify which bonds pdb2gmx is warning you about (and the atoms involved), and evaluate them with a viewer (VMD, etc). Likely the model you've constructed has some non-physical attributes. -Justin > > Thank you Justin > > -----Original Message----- > From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Date: Mon, 31 Mar 2008 15:25:11 -0400 > Subject: Re: Re: [gmx-users] error with pdb2gmx when using AMBER ff in > GROMACS > > Quoting OZGE ENGIN <[EMAIL PROTECTED]>: > > > I already indicated the problem that I have. If I put an N prefix to the > > first residue, I get warning of having "long bonds." It has been indicated > in > > the mail.Moreover, these long bonds can not be minimized during the > > minimization step. Although I put a relatively higher tolerance for the > force > > on atoms. > > Alright, that makes more sense. You didn't say before that you couldn't > resolve > the long bonds by minimization. It seemed that you were asking again about > the > N-terminal nomenclature. It sounds like your starting structure has > problems, > but without knowing more I can't comment on that. Is it something you've > built, something from the RCSB, etc? > > Have a look at your structure and the mdrun output (md.log, in particular) to > see if you can determine where things are falling apart based on specific > warnings (LINCS, etc.) > > -Justin > > > > > -----Original Message----- > > From: "Justin A. Lemkul" <[EMAIL PROTECTED]> > > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > > Date: Mon, 31 Mar 2008 14:42:55 -0400 > > Subject: Re: [gmx-users] error with pdb2gmx when using AMBER ff in GROMACS > > > > Quoting OZGE ENGIN <[EMAIL PROTECTED]>: > > > > > Hi all, > > > > > > I am trying to use AMBER ff in GROMACS. I have followed the steps that > are > > > given in the http://chemistry.csulb.edu/ffamber/ link. > > > > > > The first residue of the protein is GLN. I put an N prefix to this > residue. > > > The pdg2gmx works well except giving an warning of long bond between some > > > atoms. > > > > > > In contrast, if I have not put any prefix to GLN, then, the following > error > > > appears: > > > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > > WARNING: atom H is missing in residue GLN 1 in the pdb file > > > You might need to add atom H to the hydrogen database of residue GLN > > > in the file ff???.hdb (see the manual) > > > > > > ------------------------------------------------------- > > > Program pdb2gmx, VERSION 3.3.1 > > > Source code file: pdb2top.c, line: 697 > > > > > > Fatal error: > > > There were 1 missing atoms in molecule Protein, if you want to use this > > > incomplete topology anyhow, use the option -missing > > > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > > > > > I looked at both the .rtp and .hdb files, but everything seems to be > > correct. > > > > > > Does anybody face with a similar problem? > > > > If it is an N-terminal residue, it needs to be preceded by an 'N' (i.e., > > NGLN), > > and likewise for C-terminal residues, CXXX. This is in the documentation > > from > > the AMBER ports at the link you cite above, and the link I already provided > > you. > > > > So what's the problem? > > > > -Justin > > > > > > > > Thanks in advance > > > Ozge Engin > > > ================================= > > > Computational Science & Engineering > > > Koc University > > > _______________________________________________ > > > gmx-users mailing list gmx-users@gromacs.org > > > http://www.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 > > > > > > > > > > > ======================================== > > > > Justin A. Lemkul > > Graduate Research Assistant > > Department of Biochemistry > > Virginia Tech > > Blacksburg, VA > > [EMAIL PROTECTED] | (540) 231-9080 > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > > > ======================================== > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.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 > > > > > > Ozge Engin > > ================================= > > Computational Science & Engineering > > Koc University > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.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 > > > > > > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.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 > > > Ozge Engin > ================================= > Computational Science & Engineering > Koc University > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.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 > ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.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
