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: cseif...@bph.rub.de Web: http://www.bph.rub.de -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
