Hello Rolf, There might be some issues with the exact format, below I pasted a record from a standard pdb-file (that works with pdb2gmx) for comparison.
Otherwise for a simple molecule like methane, x2top is probably better suited than pdb2gmx to generate the topology. Best wishes Andreas > -----Original Message----- > From: [email protected] [mailto:[email protected]] > On Behalf Of Rolf Erwin Isele-Holder > Sent: 15 May 2009 09:12 > To: [email protected] > Subject: [gmx-users] pdb2gmx does not recognize residues > > Hello everybody, > > I'm trying to set up a box with methane. Therefore I wrote a small pdb file > which looks like this: > > ATOM 1 CH4 CH4 1 1.0 1.0 1.0 1.0 0.0 >From a working pdb-file: > ATOM 676 O ILE A 40 23.416 2.231 -1.229 1.00 0.00 O > ATOM 2 CH4 CH4 2 0.5 0.5 0.5 1.0 0.0 > ATOM 3 CH4 CH4 3 0.0 0.0 0.0 1.0 0.0 > END > > > Unfortunately when using bdb2gmx on this file, the message: " Residue 'C' > not found in redsidue database" is shown. > Why does gromacs not recognize that it is not supposed to look for a residue > called 'C' which does not exist, but a residue called 'CH4' which is > contained in ffG43a1.rtp ? > Does anybody know the answer? > > Greetings, Rolf > _______________________________________________ > 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 _______________________________________________ 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
