Hello I want to equilibrate the water around my (small) molecule. In the tutorials I found and in the manual is not enough information how to do that if you have an own parametrization of a molecule.
Here is my situation: I have a pdb file and I have a parametrization for this molecule out of a supporting information from a paper. I create a .rtp and .hdb file, changed atomtypes.atp, ffnonbonded.itp and residuetypes.dat. In the .rtp file I called my molecule [ ISO ] before the [ atoms ] section starts. In the residuetypes.dat file I write ISO Isoalloxazin After that I did the calculation described in the tutorial of Erik Lindahl and I got no errors up to equilibrating the water around my molecule. In my pr.mdp file is the entry tc-grps = protein non-protein I guess this is a problem because I got an error and with best thanks I got this solution from Mark Abraham: http://lists.gromacs.org/pipermail/gmx-users/2012-March/069096.html I read something about make_ndx and about Thermostats but I still have no idea how to go forward with this problem :-( Please help Thanks and greetings Lara -- 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
