Hi Grange, It recognizes the possibility of having a bond between these atoms. That's where the distance matrix comes in. But if a bond were made, you'd have a statement right after the distance matrix saying something like "linking atom ... and atom ...". It doesn't happen, and the reason is the following (you might want to search "specbond" in the user list archives): You have set your distance at 0.2 nm. pdb2gmx checks whether the actual distance is within 10% of the distance specified. The actual distance is 0.134, which lies well under the target distance. Therefore it doesn't make the bond. Try to set the bond length in specbond.dat between 0.13 and 0.14.
Hope it helps, Tsjerk On Sun, Jun 29, 2008 at 9:20 AM, Grange Hermitage <[EMAIL PROTECTED]> wrote: > Hi all, > > I am using gromacs 3.3.3, and have a specbond definition: > CHU C3 2 CHV C4 2 0.2 CHU CHV > This is recognised but not built: > 7 out of 7 lines of specbond.dat converted successfully > Special Atom Distance matrix: > CHU5 > C341 > CHV9 C472 0.134 > N-terminus: NH3+ > C-terminus: COO- > Now there are 13 residues with 123 atoms > Making bonds... > Opening library file /home/users/ghermitage/gromacs/3.3.3/top/aminoacids.dat > Number of bonds was 121, now 121 > > .top: > [ atoms ] > 48 CH1 5 CHU C3 24 0 13.019 ; qtot > -1.008 > 83 CH1 9 CHV C4 42 0 13.019 ; qtot > -2.016 > > Indeed, the bond is not built. No bond connecting the two atoms appears in [ > bonds ] > > What to do? > Thanks. > > > From ffgmx.rtp: > [ CHU ] > [ atoms ] > O O -0.669 1 > C C 0.380 1 > CA CH1 0.169 1 > N NL 0.681 1 > H H 0.004 1 > CB CH2 0.299 1 > OG OA -0.171 1 > C1 CH2 0.299 1 > C3 CH1 0.000 2 > [ bonds ] > C O > CA C > CA N > CA CB > N H > CB OG > C1 OG > C1 C3 > [ CHV ] > [ atoms ] > O O -0.669 1 > C C 0.380 1 > CA CH1 0.169 1 > N NL 0.681 1 > H H 0.004 1 > CB CH2 0.299 1 > OG OA -0.171 1 > C2 CH2 0..299 1 > C4 CH1 0.000 2 > [ bonds ] > C O > CA C > CA N > CA CB > N H > CB OG > C2 OG > C2 C4 > ________________________________ > Get the name you always wanted with the new y7mail email address. > _______________________________________________ > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ 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