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

[maria goranovic]

 Thank you all for the replies and help. The main reason I was messing with
pdb2gmx, editconf and genbox was mainly to convert my pdb into a nice .gro
format file, which I could input into grompp. I understand grompp can take a
pdb file for input as well. Does it not need any "box" information, like the
box type, or the dimensions ? If it can infer these directly from the pdb,
or these details can be specified in the .mdp file then my problems are
solved.

I will look more carefully into the -h ..

Thank you !

-Maria


Message: 6
> Date: Thu, 04 Oct 2007 03:51:27 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] getting a good .gro file from a pdb file
>        while the       topology is ready
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4703D69F.5000005 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> Hydrogen takes up volume too... your equilibration will be less
> troublesome if your whole system "fits" at the start of the equilibration.
>
> It sounds like it might be worth your while reading the introductory
> part of pdb2gmx -h, editconf -h, genbox -h, etc. so you have an idea
> what each tool is trying to do. Following a recipe without appreciating
> what you're doing is fine, until you go to change the recipe, which is
> what you're trying to do here. :-)
>
> Mark
>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 04 Oct 2007 04:04:05 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] getting a good .gro file from a pdb file
>        while the       topology is ready
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4703D995.40608 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> 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 :-)
>
> >> 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 :-)
>
> Mark
>
>
> ------------------------------
>
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> End of gmx-users Digest, Vol 42, Issue 11
> *****************************************
>



-- 
Maria G.
Technical University of Denmark
Copenhagen
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