Thank you for your answer. If I am looking at the PDB standard format and my file, I observe that I have only one number between the type of residue and coordinates, and I suppose it is the residue current number. I am indeed missing the chain identifier code, which should be of A1 Fortran format, which I don't really understand (one carachter, but I have 32 chains, so it should be minimum A2 or I2). That I could introduce. In my pdb entries I dont define any connectors. Should they be a dummy atom, with the corresponding bond, angle, dihedhral, which after that I redefine in the tdb file? I dont think it is a visualisation artefact, because it really gives less number of bonds, corresponding to the missing intermonomeric bonds.
Should I do now both (introducing a chain identifier in the pdb, but how?, and defining the intermonomeric bonds via dummy in the pdb and tdb?)? Thanks again for your help. Best regards, Andrea 2008/10/22 Mark Abraham <[EMAIL PROTECTED]> > Andrea Muntean wrote: > >> I have a *pdb file for a polymer box which I want to use. I defined the >> residues (the first, the last and the inner monomers). >> Pdb2gmx runs, but I obtain a "soup" of monomers instead of N chains a M >> monomers each. >> My problem now is how to connect the monomers. What is the best way to do >> so? >> > > We can't tell yet. You might have a PDB file with each residue in its own > chain. You might have defined residue topologies without suitable > connectors. You might be observing a visualization artefact. You might have > some warnings from pdb2gmx you haven't observed yet. > > Mark > _______________________________________________ > 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 >
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