[gmx-users] getting a good .gro file from a pdb file while the topology is ready

Allen Smith easmith at beatrice.rutgers.edu
Thu Oct 4 01:09:54 CEST 2007

In message <4703D995.40608 at anu.edu.au> (on 4 October 2007 04:04:05 +1000),
Mark.Abraham at anu.edu.au (Mark Abraham) wrote:
>Allen Smith wrote:
>> In message <9024f1330710031013t10772b86nfb62129ec625c03e at mail.gmail.com> (on
>> 3 October 2007 19:13:51 +0200), mariagoranovic at gmail.com (maria goranovic)
>> wrote:
>>> Hi,
>>> I had a large bilayer in .gro and .top gromacs format files
>> Bilayer? I believe there are some specific things for doing planar periodic
>> boundary conditions (or planar infinite system conditions), but I am not
>> familiar with them.
>Yeah but they're in the .mdp and not the issue here :-)

Ah, thank you.

>>> which I truncated to make a smaller bilayer, and added some more water
>>> molecules, using programs other than gromacs. The final output I have is a
>>> pdb file with complete solvation, and a topology file which I obtained from
>>> the original top file by simply changing the number of residues of each
>>> group in the last section.
>> Umm... the atom numbers (not just the numbers of residues) are going to need
>> to correspond between the .top and .gro files.
>I think the OP meant changing the number of molecules in the [molecules] 
>section of the .top file. I expect that within each molecule in the 
>structure file the order of the atoms must agree between with the 
>topology file. Certainly the order of the molecules in the [molecules] 
>section must correspond to that in the structure file.
>However, the atom numbers cannot (in general), match in order between 
>structure and topology file for any system with more than one copy of a 
>molecule (e.g. solvent). For simple solvated systems where one gets 
>focussed on the solute, it can look like correspondence is occurring and 
>thus might be necessary :-)

However, in this case, the original poster has not only edited down the
solvent, but the bilayer. I am reasonably certain that if I put in more than
one copy of something which is in a .rtp file and _not_ in, say, ions.itp,
then it will be in both times in the .top file (after all, two
different-position glycines are in twice in the .top file...). There may be
some dependence on chain labels from the original .pdb file, however, from
observations; I suppose that it's possible that it would partially depend on
whether the name is in aminoacid.dat or something like that, although that
seems a bit weird. It doesn't sound like the original poster is using
something that's in an .itp file that the original poster has constructed.


P.S. Incidentally, I note the irritating habit of pdb2gmx (including in
3.3.2) of converting what is already labeled as SOL to HOH, even though
genbox inserts water molecules as SOL.

Allen Smith			         http://cesario.rutgers.edu/easmith/
There is only one sound argument for democracy, and that is the argument
that it is a crime for any man to hold himself out as better than other men,
and, above all, a most heinous offense for him to prove it. - H. L. Mencken

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