Yes, it is possible by deveoping your own topology. Pdb2gmx is not suitable for that purpose.
It would be helpful to check out the documentation resources and manual, e.g. http://wiki.gromacs.org/index.php/FAQs x2top and the prodgr web-server might be some good starting points. Andreas >>>>> From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Bernhard Knapp Sent: 19 November 2008 12:54 To: gmx-users@gromacs.org Subject: [gmx-users] sedoheptulose Dear users I would like to perform a MD simulation of Sedoheptulose (C7H14O7) via Gromacs. But already during pdb2gmx it comes up with: "Residue 'UNK' not found in residue topology database" which is obviously clear since sedoheptulose is not an amino acid. Is it somehow possible to simulate this molecule? the sedoheptulose data to start from is: ATOM 1 C UNK 0 -3.442 2.742 0.000 0.00 0.00 C+0 ATOM 2 C UNK 0 -2.108 3.512 0.000 0.00 0.00 C+0 ATOM 3 C UNK 0 -0.774 2.742 0.000 0.00 0.00 C+0 ATOM 4 C UNK 0 0.559 3.512 0.000 0.00 0.00 C+0 ATOM 5 C UNK 0 1.893 2.742 0.000 0.00 0.00 C+0 ATOM 6 C UNK 0 3.227 3.512 0.000 0.00 0.00 C+0 ATOM 7 O UNK 0 -0.774 1.202 0.000 0.00 0.00 O+0 ATOM 8 O UNK 0 0.559 5.052 0.000 0.00 0.00 O+0 ATOM 9 O UNK 0 1.893 1.202 0.000 0.00 0.00 O+0 ATOM 10 O UNK 0 -4.775 3.512 0.000 0.00 0.00 O+0 ATOM 11 O UNK 0 -2.108 5.052 0.000 0.00 0.00 O+0 ATOM 12 H UNK 0 -6.109 2.742 0.000 0.00 0.00 H+0 ATOM 13 H UNK 0 -0.774 5.822 0.000 0.00 0.00 H+0 ATOM 14 H UNK 0 1.893 5.822 0.000 0.00 0.00 H+0 ATOM 15 H UNK 0 0.559 0.432 0.000 0.00 0.00 H+0 ATOM 16 H UNK 0 3.227 0.432 0.000 0.00 0.00 H+0 ATOM 17 C UNK 0 4.560 2.742 0.000 0.00 0.00 C+0 ATOM 18 O UNK 0 5.894 3.512 0.000 0.00 0.00 O+0 ATOM 19 H UNK 0 7.228 2.742 0.000 0.00 0.00 H+0 ATOM 20 O UNK 0 3.227 5.052 0.000 0.00 0.00 O+0 cheers bernhard _______________________________________________ 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
