[gmx-users] Equilibrate the water around my molecule

Lara Bunte lara.bunte at yahoo.de
Mon Mar 26 14:55:05 CEST 2012


my command was pdb2gmx -f isoalloxazin.pdb -water tip3p which worked for ISO Isoalloxazin in the residuetypes.dat

I don't get an output of this command, only the fatal error I wrote and an empty topology file.

I don't know what to do now


----- Ursprüngliche Message -----
Von: Mark Abraham <Mark.Abraham at anu.edu.au>
An: Discussion list for GROMACS users <gmx-users at gromacs.org>
Gesendet: 14:45 Montag, 26.März 2012
Betreff: Re: [gmx-users] Equilibrate the water around my molecule

On 26/03/2012 11:21 PM, Lara Bunte wrote:
> 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?

Please get in the habit of supplying the command line you used. Various 
symptoms can have multiple causes, and retaining information does not 
help you.

Because ISO is now protein, pdb2gmx knows to expect to have to deal with 
terminating the residue chain (pehaps building in terminal atoms, such 
as OXT). Or not, according to what is needed in your case. See pdb2gmx 
-h regarding the -ter option. Be sure to read and understand the pdb2gmx 
output - it probably talked about the termini.


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

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