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

[Justin A. Lemkul]

You can use editconf to directly convert a .pdb file into .gro format.

-Justin

Quoting maria goranovic <mariagoranovic at gmail.com>:

>  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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> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> >
> > End of gmx-users Digest, Vol 42, Issue 11
> > *****************************************
> >
>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
>



======================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://bevanlab.biochem.vt.edu/Pages/Personal/justin/

======================