[gmx-users] Equilibrate the water around my molecule

Lara Bunte lara.bunte at yahoo.de
Mon Mar 26 14:21:12 CEST 2012


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?


----- Ursprüngliche Message -----
Von: Mark Abraham <Mark.Abraham at anu.edu.au>
An: Discussion list for GROMACS users <gmx-users at gromacs.org>
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.

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