Hi everybody, I try to use GROMACS for my protein where I added a layer of dummy atoms simulating the membrane around it. But now when I want to call "pdb2gmx" I always get the error: Fatal error: Residue 'DUM' not found in residue topology database I understand the error, that there is no entry for the dummy residue in the .tpr file. But is there a possibility to add it there. Because the file don't look like that I can just write "DUM" in it.
my pdb file looks like this: ATOM 2597 CB LEU A 313 12.816 -29.877 -23.547 1.00 55.31 C ATOM 2598 CG LEU A 313 14.261 -29.695 -23.059 1.00 54.06 C ATOM 2599 CD1 LEU A 313 15.169 -30.640 -23.866 1.00 53.26 C ATOM 2600 CD2 LEU A 313 14.757 -28.257 -23.179 1.00 54.46 C TER HETATM 3076 DUM DUM A 314 -4.000 -49.000 6.000 1.00 1.70 HETATM 3077 DUM DUM A 314 -4.000 -49.000 7.000 1.00 1.70 HETATM 3078 DUM DUM A 314 -4.000 -48.000 6.000 1.00 1.70 HETATM 3079 DUM DUM A 314 -4.000 -48.000 7.000 1.00 1.70 . . . . HETATM 36213 O HOH A 527 25.281 -35.299 13.147 1.00 37.03 O HETATM 36214 O HOH A 528 46.452 -27.955 -20.733 1.00 19.63 O HETATM 36215 O HOH A 530 32.439 -23.614 -26.720 1.00 27.12 O TER Best regards, Eva -- 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