dear gromacs users im using gromacs to make CS2 MD programs i made pdb file (by converting mol file to pdb file) and rtp file for CS2this is what i made <pdb file> COMPND UNNAMEDAUTHOR GENERATED BY OPEN BABEL 2.3.2HETATM 1 C LIG 1 19.882 -4.263 -0.027 1.00 0.00 C HETATM 2 S LIG 1 21.256 -5.103 -0.054 1.00 0.00 S HETATM 3 S LIG 1 18.508 -3.424 0.000 1.00 0.00 S CONECT 1 2 3 CONECT 2 1 CONECT 3 1 MASTER 0 0 0 0 0 0 0 0 3 0 3 0END ------------------------------------------------------------------------------------- <rtp file> [ LIG ] [ atoms ]C opls_77 0 0S1 opls_202 0 0S2 opls_202 0 0 [ bonds ]C S1C S2 i attached rtp file to /usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp andi added it to residuetypes.dat (which is in /usr/share/gromacs/top)then i wrote command pdb2gmx to make gro file but it failed Fatal error:Atom type opls_77 (residue LIG) not found in atomtype databaseFor more information and tips for troubleshooting, please check the GROMACSwebsite at http://www.gromacs.org/Documentation/Errors before i made rtp file, i checked atomtypes atp file which is in oplsaa.ff it says olps_77 is carbon(isobutene) and opls_202 is sulfides i dont know why gromacs cant find atom type opls_77 also, to make rtp file how to give charge and charge group to each atoms? someone who knows about this, please help me thank you so much
-- View this message in context: http://gromacs.5086.x6.nabble.com/cant-find-certain-atomtypes-from-atomtype-database-tp5011944.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists