Dear Ladies and Gentlemen, I from the University of Applied Sciences in Mittweida currently deals with the calculation of a propene molecule using the program Gromacs. For testing proposer I tried to generate my own force field. However, when creating the top-file with this command "grompp_d -f propene.mdp -c propene_new.gro -p propene.top -o propene.tpr -po propene_new.mdp" the following error messages was generated: No default Bond types No default Angle types
The original pdb file before adding the water solvent was: COMPND PROPENE ATOM 2 C CH33 1 3.732 0.250 0.000 1.00 0.00 ATOM 2 H1 CH33 1 4.042 -0.286 0.000 1.00 0.00 ATOM 2 H2 CH33 1 4.269 0.560 0.000 1.00 0.00 ATOM 2 H3 CH33 1 3.422 0.786 0.000 1.00 0.00 ATOM 2 C1 C2H3 2 2.866 -0.250 0.000 1.00 0.00 ATOM 2 C2 C2H3 2 2.000 0.250 0.000 1.00 0.00 ATOM 2 H1 C2H3 2 2.866 -0.870 0.000 1.00 0.00 ATOM 2 H2 C2H3 2 2.000 0.870 0.000 1.00 0.00 ATOM 2 H3 C2H3 2 1.463 -0.060 0.000 1.00 0.00 I derived the own force field from ffamber99. In the rtp file I have added: [CH33] [Atom] C amber99_2 0.880229 1 H1 amber99_17 0.395055 2 H2 amber99_17 0.395055 3 H3 amber99_17 0.395055 4 [bonds] C H1 C H2 C H3 [C2H3] [Atom] C1 amber99_70 0.880229 1 C2 amber99_71 0.880229 2 H1 amber99_17 0.395055 3 H2 amber99_17 0.395055 4 H3 amber99_17 0.395055 5 [bonds] C1 C2 C1 H1 C2 H2 C2 H3 In the itp file we have added: [atom type] amber99_70 -> parameters like amber99_2 amber99_71 -> parameters like amber99_2 [bond type] i j func b0 kb C C1 1 0.1525 259408.0; new99 C1 C2 1 0.1525 259408.0; new99 C1 H1 1 0.1525 259408.0; new99 C2 H2 1 0.1525 259408.0; new99 C2 H3 1 0.1525 259408.0; new99 I would like to ask whether you could help me to solve the problems. Also any other hint on the creation/implementation of my own force field is welcome. Thank you for your efforts. Yours sincerely, Saskia Frenzel -- Neu: GMX FreeDSL Komplettanschluss mit DSL 6.000 Flatrate + Telefonanschluss für nur 17,95 Euro/mtl.!* http://dslspecial.gmx.de/freedsl-surfflat/?ac=OM.AD.PD003K11308T4569a -- Psssst! Schon vom neuen GMX MultiMessenger gehört? Der kann`s mit allen: http://www.gmx.net/de/go/multimessenger01 -- Psssst! Schon vom neuen GMX MultiMessenger gehört? Der kann`s mit allen: http://www.gmx.net/de/go/multimessenger01 _______________________________________________ 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
