Hi I changed in my residuetypes.dat file ISO Isoalloxazin in ISO Protein. I want to repeat the calculations I did before by pdb2gmx it already failed. I got the error:
Fatal error: Atom OXT in residue ISO 1 was not found in rtp entry ISO with 32 atoms while sorting atoms. I have no shortcut OXT in my molecule parametrization. What is the problem? Greetings Lara ----- Ursprüngliche Message ----- Von: Mark Abraham <[email protected]> An: Discussion list for GROMACS users <[email protected]> CC: Gesendet: 19:55 Freitag, 23.März 2012 Betreff: Re: [gmx-users] Equilibrate the water around my molecule On 24/03/2012 5:38 AM, Lara Bunte wrote: > 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 The above entry in residuetypes.dat makes it impossible for GROMACS to recognise your ISO as protein. See manual 8.1.1. This file identifies the *type* of the *residue* to permit GROMACS and you to agree on broad categorizations of residues. Telling GROMACS the full name of the molecule is not helpful here. > 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 Here you require a protein group to exist. Apparently you have no part of your system that is protein according to residuetypes.dat, and so there is no such group. If you'd had another protein element to your system, then grompp would have regarded ISO as non-protein, and you might have been left with a hard-to-notice problem. > > 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 :-( All three forms of solution I proposed there are still possible. The second is the easiest: use "ISO Protein" in your residuetypes.dat. Mark -- 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 -- 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
