Dear Gmx Users, I created my own CG force field and i process my structure to pdb2gmx. I process 3 beads I created to check whether the topology is properly created:
Using the CG force field in directory ./CG.ff No file 'watermodels.dat' found, will not include a water model Reading 60central_Carbons.pdb... Read 3 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 1 chains and 0 blocks of water and 3 residues with 3 atoms chain #res #atoms 1 'X' 3 3 All occupancy fields zero. This is probably not an X-Ray structure Opening force field file ./CG.ff/atomtypes.atp Atomtype 1 Reading residue database... (CG) Opening force field file ./CG.ff/aminoacids.rtp Reading .rtp file without '[ bondedtypes ]' directive, Will proceed as if the entry [ bondedtypes ] ; bonds angles dihedrals impropers all_dihedrals nr_exclusions HH14 remove_dih 1 1 1 2 0 3 1 1 Residue 13t at the beginning of ./CG.ff/aminoacids.rtp Sorting it all out... Back Off! I just backed up topol.top to ./#topol.top.2# Processing chain 1 'X' (3 atoms, 3 residues) Identified residue MET1 as a starting terminus. Identified residue VAL3 as a ending terminus. 8 out of 8 lines of specbond.dat converted successfully Checking for duplicate atoms.... Now there are 3 residues with 3 atoms Making bonds... No bonds Generating angles, dihedrals and pairs... Making cmap torsions...There are 0 dihedrals, 0 impropers, 0 angles 0 pairs, 0 bonds and 0 virtual sites Total mass 319.420 a.m.u. Total charge 1.000 e Writing topology Back Off! I just backed up posre.itp to ./#posre.itp.2# Writing coordinate file... Back Off! I just backed up 60proc.pdb to ./#60proc.pdb.2# --------- PLEASE NOTE ------------ You have successfully generated a topology from:3Carbons.pdb. The CG force field is used. --------- ETON ESAELP ------------ gcq#304: "Gabba Gabba Hey!" (The Ramones) It stated that there are no angles. However in my ffbonded.itp which i ncluded in my forcefield.itp [ angletypes ] ; i j k funct th0 C0 C1 C2 C3 C4 CME CSE CVA 6 0 0.0680894 -0.0328291000 590330 -46.3 13 How Gromacs can read this angle? In terms of bonds I want to use constraints, can I use in my ffbonded.itp [ costrainttypes] or add them automatically after? Steven -- 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