> dear dean, there is no problem with your mdp file. for grompp number of atoms in .top file and input .gro file should be equal,look your.top file, this may be because u have added number of ions in your .top file but it not present in your .gro file( difference of 8 atom only in both file, which equal to no of ions u have to aded for nutrilizing your system). look both file and try to manage. sanjay
Send gmx-users mailing list submissions to > gmx-users@gromacs.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.gromacs.org/mailman/listinfo/gmx-users > or, via email, send a message with subject or body 'help' to > gmx-users-requ...@gromacs.org > > You can reach the person managing the list at > gmx-users-ow...@gromacs.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of gmx-users digest..." > > > Today's Topics: > > 1. Re: Problem with adding H using amber03 (Justin A. Lemkul) > 2. NVT or NPT ? (Chih-Ying Lin) > 3. NVT or NPT ? (chris.ne...@utoronto.ca) > 4. RE: anomalous free energy dgdl.xvg values every nstlist steps > while using a twin-range cutoff (Berk Hess) > 5. grompp error- Excluding 3 bonded neighbours-Fatal error > (Dean Cuebas) > 6. Re: NVT or NPT ? (Tsjerk Wassenaar) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 17 Feb 2009 20:43:09 -0500 > From: "Justin A. Lemkul" <jalem...@vt.edu> > Subject: Re: [gmx-users] Problem with adding H using amber03 > To: Discussion list for GROMACS users <gmx-users@gromacs.org> > Message-ID: <499b67ad.9010...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > Peggy Yao wrote: >> Dear all, >> >> I am trying to use amber03 force field. I corrected the amino acid names >> as described on http://chemistry.csulb.edu/ffamber/. >> >> However, when I ran pdb2gmx on a PDB file without H-atoms, I got the >> following error: >> >> pdb2gmx -ff amber03 -f protein_without_H.pdb -o protein_amber03.pdb >> >> ... >> WARNING: atom H is missing in residue THR 1 in the pdb file >> You might need to add atom H to the hydrogen database of >> residue THR >> in the file ff???.hdb (see the manual) >> > > Obviously you did not follow all of the directions. If Thr is amino acid > 1 > (i.e., the N-terminus) it should be called NTHR. > > -Justin > >> >> ------------------------------------------------------- >> Program pdb2gmx, VERSION 4.0.2 >> Source code file: pdb2top.c, line: 701 >> >>%2 _______________________________________________ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
