Hi, one possible reason could be that the files are not included correctly. Check the -pp output. Otherwise it is difficult to tell without the files.
Roland On Fri, Oct 8, 2010 at 5:48 AM, Christian Seifert < [email protected]> wrote: > Hi GMXers, > > this is a Mail from one of my colleagues (who is not yet member of > this ) > Hi GMXers, > > a colleague of mine (who is not yet member of our enlightened list, but > maybe I can convince him, if we find a solution.. ^^) has a problem > after he had copied functioning CHARMM parameters to GMX. I tried to > solve the problem, but my trained knowledge on parameterization of OPLS > parameters in GMX 4.0 was obviously not sufficient for CHARMM and GMX > 4.5. > > Greets, > Christian > > > Dear Users, > > After using the > > grompp -v -f minim.mdp -c hpgk_open_adp_bpg-water.gro -p > hpgk_open_adp_bpg.top -o hpgk_open_adp_bpg-water.tpr > > Gromacs command, I got the following error message from grompp > > Program grompp, VERSION 4.5.1 > > Source code file: ../../../gromacs-4.5.1/src/kernel/toppush.c, line: 631 > > Fatal error: > > Unknown bond_atomtype CN7 > > I have a system of a protein in complex with two substrates: ADP and > BIPG (bis-phosphoglycerate). I am using the CHARMM27 force field. I have > added new parameters for BIPG in the corresponding .itp files (bonded > paramerers to ffnabonded.itp and non-bonded parameters to > ffnanonbonded.itp). All the atomtypes of BIPG are defined in > atomtypes.atp. I have built the topology for BIPG in .rtp file and > hyrodgen data base file .hdb as well. Moreover I have added BIPG as new > residue in the residuetypes.dat file. I have created succesfully a .top > file for my system and molecule.itp files for the protein and each > substrates by pdb2gmx. The .top and molecule.itp files are in accordance > with the rtp files. However grompp cannot recognize the bond parameter > for the CN7 atom of BIPG. Is there any idea to solve this problem? > > > Thank you in advance, > > Zoltan Palmai > > -- > M.Sc. Christian Seifert > Department of Biophysics > University of Bochum > ND 04/67 > 44780 Bochum > Germany > Tel: +49 (0)234 32 28363 > Fax: +49 (0)234 32 14626 > E-Mail: [email protected] > Web: http://www.bph.rub.de > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
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