It did work. Thank you! Cheers, Andrea
2008/10/23 Mark Abraham <[EMAIL PROTECTED]> > Andrea Muntean wrote: > >> 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. >> > > Get a PDB file with just one polymer molecule and work on getting a > topology for that. Walking before running :-) > > 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? >> > > First you need a functional *residue topology*. Check chapter 5 of the > manual and look at the other force fields to see how (for example) protein > force fields define the connectors with + and - prefixes. Once you've got > that, then it's possible for pdb2gmx to join them head to tail (using the > residue number field to indicate the breaks, and the name to match up with > the topology you've defined), and you may then need either terminating > residues of a different name or a .tdb entry. > > I dont think it is a visualisation artefact, because it really gives less >> number of bonds, corresponding to the missing intermonomeric bonds. >> > > Your visualization software is not reading a file format that is encoding > any topology (since you haven't produced one yet). Thus it's inventing some > bonds based on the coordinates. The output of pdb2gmx that contains topology > information is the .top file, not the coordinate file. > > 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?)? >> > > I suppose there are some circumstances where chain identifiers might be > useful, but since you haven't even told us what your monomer and system are, > it's hard to help you. > > > Mark > _______________________________________________ > gmx-users mailing list [email protected] > 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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