Thanks a lot Justin. It worked really nice. now I am stuck with another problem. I need to add the Building block GTP and GDP in 43a1, as I need to get the topology of a tubulin monomer. I got the file from a old post here.
http://www.gromacs.org/pipermail/gmx-users/2005-May/015188.html I copied and pasted it into my file, yet, as the structure doesn't match it gave several errors. is there any way to fix this? Thanks a lot for your help. Tawhid ----- Original Message ---- From: Justin A. Lemkul <[EMAIL PROTECTED]> To: Discussion list for GROMACS users <gmx-users@gromacs.org> Sent: Monday, November 26, 2007 7:14:43 PM Subject: Re: [gmx-users] pdb2gmx error Quoting Tawhid Ezaz <[EMAIL PROTECTED]>: > Hi, > > I have just started to learn gromacs. I am facing a problem to make topology > file of a myoglobin. I got the pdb file from the csc tutorial. > > When i am running the pdb2gmx with > > pdb2gmx -f conf.pdb -p topol.top > > i get the message, HEME148 CAB1428 0.569 > HEME148 CAC1437 0.562 0.820 > N-terminus: NH3+ > C-terminus: COO- > Now there are 148 residues with 1451 atoms > ------------------------------------------------------- > Program pdb2gmx, VERSION 3.3.1 > Source code file: pdb2top.c, line: 570 > > Fatal error: > atom N not found in residue 1ACE while combining tdb and rtp > ------------------------------------------------------- > > I was using 43a1 force field (0), {but none of them works}. > > i read some previous post and got the idea that there should be a N atom with > should be linked with ACE, but my conf.pdb files does not have any. I have > topol.top file from the tutorial but didn't show how I can generate that. Use the -ter option with pdb2gmx, and select 'none' when prompted. That way, pdb2gmx does not look for an N-terminal nitrogen (which is obviously absent in an acetyl group). -Justin > > I am a totally newbie, thus I am wondering what should I do. Which file I > should correct to get rid of those? Do I need to know the bonding of every > atom in the molecule for that? > > Thanks in advance > > Tawhid > > > > > ======================================== 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
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