Thank you very much for this detailed answer!! > 'pdb2gmx' is mainly a tool to get the topology for (bigger) molecules > from a *.pdb file. 'pdbgmx' is expecting an entry in the *.rtp file for > the dummy atoms. You could add one in that file... (see further below) > > But if the dummys only interact via nonbonded interactions it would be > more convient to write the topology by hand. > In the *.top file, you would need after the protein a new entry with > [ moleculetype ] > and > [ atoms ] > But you should also have this nonbonded interaction in the *nb.itp and > file of your force field and the atom definition in the *.atp file. > > > If there are also bonded parameters the new *.rtp entry would be better. > For this look at the definition of an aminoacid, or a single molecule > and write something similar for your dummy atoms. > Essential you would need the atoms definitions and charges, and then an > entry for which atoms is bonded to which. > > But you should also have these interactions (nonbonded and bonded) in > the *nb.itp and *bon.itp files of your force field and the atom > definition in the *.atp file. > > The basic informations for both ways are in chapter 5 of the manual. > > Hope this gives some hints. > Greetings > Thomas Schlesier > > > > Am 20.06.2012 16:18, schrieb gmx-users-requ...@gromacs.org: >> Hi everybody, >> >> I try to use GROMACS for my protein where I added a layer of dummy atoms >> simulating the membrane around it. >> But now when I want to call "pdb2gmx" I always get the error: >> Fatal error: >> Residue 'DUM' not found in residue topology database >> I understand the error, that there is no entry for the dummy residue in >> the .tpr file. But is there a possibility to add it there. Because the >> file don't look like that I can just write "DUM" in it. >> >> >> my pdb file looks like this: >> >> ATOM 2597 CB LEU A 313 12.816 -29.877 -23.547 1.00 55.31 >> C >> ATOM 2598 CG LEU A 313 14.261 -29.695 -23.059 1.00 54.06 >> C >> ATOM 2599 CD1 LEU A 313 15.169 -30.640 -23.866 1.00 53.26 >> C >> ATOM 2600 CD2 LEU A 313 14.757 -28.257 -23.179 1.00 54.46 >> C >> TER >> HETATM 3076 DUM DUM A 314 -4.000 -49.000 6.000 1.00 1.70 >> HETATM 3077 DUM DUM A 314 -4.000 -49.000 7.000 1.00 1.70 >> HETATM 3078 DUM DUM A 314 -4.000 -48.000 6.000 1.00 1.70 >> HETATM 3079 DUM DUM A 314 -4.000 -48.000 7.000 1.00 1.70 >> . >> . >> . >> . >> HETATM 36213 O HOH A 527 25.281 -35.299 13.147 1.00 37.03 >> O >> HETATM 36214 O HOH A 528 46.452 -27.955 -20.733 1.00 19.63 >> O >> HETATM 36215 O HOH A 530 32.439 -23.614 -26.720 1.00 27.12 >> O >> TER >> >> >> >> >> >> >> Best regards, >> Eva > > -- > 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 >
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