Hello group users,
I am trying to prepare a protein using the pdb2gmx module of gromacs.I have stripped the hydrogens using a different program and using a pdb file as the input.I am getting the following error message. Please help me with your suggestions on this. Thank you kindly. Select the Force Field: 0: GROMOS96 43a1 force field 1: GROMOS96 43b1 vacuum force field 2: GROMOS96 43a2 force field (improved alkane dihedrals) 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205) 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals) 7: [DEPRECATED] Gromacs force field (see manual) 8: [DEPRECATED] Gromacs force field with hydrogens for NMR 9: Encad all-atom force field, using scaled-down vacuum charges 10: Encad all-atom force field, using full solvent charges 0 Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/ffG43a1.rtp Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/aminoacids.dat Reading 1YSI_orient_chop2_protein_noH.pdb... Read 1307 atoms Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/xlateat.dat 26 out of 26 lines of xlateat.dat converted succesfully Analyzing pdb file There are 1 chains and 0 blocks of water and 163 residues with 1307 atoms chain #res #atoms 1 'A' 163 1307 All occupancies are one Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/ffG43a1.atp Atomtype 50 Reading residue database... (ffG43a1) Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/ffG43a1.rtp Residue 96 Sorting it all out... Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/ffG43a1.hdb Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/ffG43a1-n.tdb Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/ffG43a1-c.tdb Back Off! I just backed up j.top to ./#j.top.1# Processing chain 1 'A' (1307 atoms, 163 residues) There are 247 donors and 258 acceptors There are 294 hydrogen bonds Will use HISB for residue 77 Will use HISB for residue 141 Checking for duplicate atoms.... Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/specbond.dat 5 out of 5 lines of specbond.dat converted succesfully N-terminus: NH3+ C-terminus: COO- Now there are 163 residues with 1693 atoms Making bonds... Opening library file /usr/local/appl/gromacs-3.3.1/share/gromacs/top/aminoacids.dat Number of bonds was 1726, now 1723 Generating angles, dihedrals and pairs... Before cleaning: 2697 pairs ------------------------------------------------------- Program pdb2gmx, VERSION 3.3.1 Source code file: pgutil.c, line: 87 Fatal error: Atom N not found in residue 1 while adding improper ------------------------------------------------------- "Torture You.... Yeah, That's a Good Idea, I Like That." (Pulp Fiction) Prasenjit Kumar Mukherjee Graduate Student Department of Medicinal Chemistry School of Pharmacy University of Mississippi USA Cell - 662 380 0146 Office - 662 915 1286 _______________________________________________ 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
