Hi, Okay, they're read in some cases. But not in pdb2gmx related to building a topology as far as I can see. I should've written:
pdb2gmx doesn't distinguish between ATOM and HETATM entries. pdb2gmx does not read CONECT records. Now the 'TER' recoord... That makes a difference. Cheers, Tsjerk On Thu, Jan 14, 2010 at 9:23 PM, Erik Marklund <er...@xray.bmc.uu.se> wrote: > Tsjerk Wassenaar skrev: >> >> Hi Jack, >> >> On Thu, Jan 14, 2010 at 5:41 PM, Jack Shultz <j...@drugdiscoveryathome.com >> <mailto:j...@drugdiscoveryathome.com>> wrote: >> >> Problem Solved. >> I replaced HETATM with ATOM, I fixed BOTH N-terminal and >> C-terminal. I kept TER and END. Removed all CONECT. Renamed the >> CYS to CYS2. No other non-AminoAcid residues were present. Most of >> this is described by the FFAmber site >> http://chemistry.csulb.edu/ffamber/ >> >> >> Gromacs doesn't distinguish between ATOM and HETATM entries. >> Gromacs does not read CONECT records. >> Now the 'TER' recoord... That makes a difference. > > I may be wrong, but I think Gromacs reads CONNECT records nowadays. > > /Erik >> >> Cheers, >> >> Tsjerk >> >> >> -- >> Tsjerk A. Wassenaar, Ph.D. >> >> Computational Chemist >> Medicinal Chemist >> Neuropharmacologist >> > > > -- > ----------------------------------------------- > Erik Marklund, PhD student > Laboratory of Molecular Biophysics, > Dept. of Cell and Molecular Biology, Uppsala University. > Husargatan 3, Box 596, 75124 Uppsala, Sweden > phone: +46 18 471 4537 fax: +46 18 511 755 > er...@xray.bmc.uu.se http://xray.bmc.uu.se/molbiophys > > -- > gmx-users mailing list gmx-us...@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 > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- 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
