[gmx-users] Equilibrate the water around my molecule

[Mark Abraham]

On 26/03/2012 11:55 PM, Lara Bunte wrote:
> Hi
>
> my command was pdb2gmx -f isoalloxazin.pdb -water tip3p which worked for ISO Isoalloxazin in the residuetypes.dat

Sure, because pdb2gmx had not been told that ISO was protein, it didn't 
try to treat it as protein.

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

pdb2gmx writes a lot of information to the terminal output. That's 
intended to be read :-) Probably there are clues in there that indicate 
that it is trying to add/fix charged termini to your ISO molecule, which 
is the default given your command line above. Only you know whether it 
needs to do that, based on the contents of your coordinate file. If not, 
tell it not to change the termini by using pdb2gmx -ter.

Doing some tutorial material on normal protein systems would have 
acquainted you with the -ter mechanism. If you haven't done some, it 
might be a good idea.

Mark

> I don't know what to do now
>
> 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<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