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.
-----Original Message----- From: "Justin A. Lemkul" <[EMAIL PROTECTED]> To: Discussion list for GROMACS users <[email protected]> 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 [email protected] > 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 [email protected] 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 [email protected] 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
