Hi Justin, yes I have already seen this site, but want I meant is that I have no idea which values I should set. Is there something like a standard for dummy protein for membrane? Eva > > > On 6/20/12 10:17 AM, [email protected] wrote: >> 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. >> >> > > http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field > > -Justin > >> 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 >> > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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