hello everybody i had sent this mail before but was not accepted because of a large attachemnt (top file). now i`m sending it again without any attachment.
i`m trying to simulate a double helical DNA using gromacs 3.3 with G43a1 force field. for this i modified the residue names in the pdb file and converted the file the gromacs format using pdb2gmx command. then i set the simulation box using editconf. now on preprocessing the files with grompp i`m getting following error processing topology... Generated 279 of the 1225 non-bonded parameter combinations WARNING 1 [file "1blo_dna_p2g.top", line 4832]: No default Proper Dih. types, using zeroes WARNING 2 [file "1blo_dna_p2g.top", line 4849]: No default Proper Dih. types, using zeroes WARNING 3 [file "1blo_dna_p2g.top", line 4866]: No default Proper Dih. types, using zeroes WARNING 4 [file "1blo_dna_p2g.top", line 4883]: No default Proper Dih. types, using zeroes WARNING 5 [file "1blo_dna_p2g.top", line 4900]: No default Proper Dih. types, using zeroes WARNING 6 [file "1blo_dna_p2g.top", line 4916]: No default Proper Dih. types, using zeroes WARNING 7 [file "1blo_dna_p2g.top", line 4932]: No default Proper Dih. types, using zeroes WARNING 8 [file "1blo_dna_p2g.top", line 4948]: No default Proper Dih. types, using zeroes WARNING 9 [file "1blo_dna_p2g.top", line 4965]: No default Proper Dih. types, using zeroes WARNING 10 [file "1blo_dna_p2g.top", line 4982]: No default Proper Dih. types, using zeroes Cleaning up temporary file gromppMWjN6A ------------------------------------------------------- Program grompp, VERSION 3.3 Source code file: fatal.c, line: 416 Fatal error: Too many warnings, grompp terminated ------------------------------------------------------- googling through the mail archive i found that prodrg server might help. but i not sure which of the output file generated by the server to be used and how exactly to use them since the another strange thing about the pdb files generated by prodrg output is that it changes the residues names and also represents the ATOM as HETATM. kindly help me solve this problem best regards, Manish Datt Research Scholar Bioinformatics Centre Institute of Microbial Technology Sector 39A, Chandigarh-160036 India. _______________________________________________ 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
