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.
Mark
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
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