> Thanks for the valueable suggessions, but sir i am actually > want to use this > program for small molecules. I have taken single FAD molecule as u > suggested modified the atom type as described in ffgmx.rtp, > program results > top and gro files using pdb2gmx, but while running grompp i > am getting the > error: > > Back Off! I just backed up mdout.mdp to ./#mdout.mdp.10# > checking input for internal consistency... calling > /usr/bin/cpp... processing topology... Generated 1284 of the > 1485 non-bonded parameter combinations WARNING 1 [file > "fad.top", line 128]: > No default Bond types, using zeroes > WARNING 2 [file "fad.top", line 139]: > No default Bond types, using zeroes > WARNING 3 [file "fad.top", line 141]: > No default Bond types, using zeroes > WARNING 4 [file "fad.top", line 328]: > No default Angle types, using zeroes > WARNING 5 [file "fad.top", line 329]: > No default Angle types, using zeroes > WARNING 6 [file "fad.top", line 334]: > No default Proper Dih. types, using zeroes > WARNING 7 [file "fad.top", line 336]: > No default Proper Dih. types, using zeroes > WARNING 8 [file "fad.top", line 338]: > No default Proper Dih. types, using zeroes > WARNING 9 [file "fad.top", line 341]: > No default Proper Dih. types, using zeroes > WARNING 10 [file "fad.top", line 343]: > No default Proper Dih. types, using zeroes > Cleaning up temporary file gromppLLm3l8 > ------------------------------------------------------- > Program grompp, VERSION 3.3.1 > Source code file: fatal.c, line: 416 > Fatal error: > Too many warnings, grompp terminated > ------------------------------------------------------- > "I Need Love, Not Games" (Iggy Pop & Kate Pierson)
Those errors mean exactly what they say, you have no definition (in the forcefield that you have used) for those bonds, angle and proper dihedral types. > Moreover , suppose if we want to use this program (grompp) for say, a > molecule which has no entry in any .rtp file provided with > Gromacs and we grompp doesn't use the .rtp files, that is for pdb2gmx. > use the PRODRG server, then how to deal with the error > "invalid molecular > directive type". Amazing what you can find by searching the emailing list ;) http://www.gromacs.org/external/search.html http://www.gromacs.org/pipermail/gmx-users/2006-November/024540.html http://www.gromacs.org/pipermail/gmx-users/2003-December/008346.html Might be an idea to have a read through the manual as well, particularly the chapters on topologies. _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
