[gmx-users] Restraining two Macromolecules
Arman Mahboubi Soufiani
armansoufiani at gmail.com
Thu Oct 18 00:33:16 CEST 2012
I greatly appreciate your kind and thorough response.
I should say that not only I got the point that I was looking for but also
I learnt much more of your explanations.
On Thu, Oct 18, 2012 at 1:35 AM, Paulo Netz <paulo.netz at gmail.com> wrote:
> It depends on how the molecules are defined in the topology file.
> If the coordinates of both molecules are contained in the main
> part of the topology file, only one position restraint file is enough
> and it should contain entries for all the non-hydrogen atoms in
> both molecules. However, if the coordinates of only
> one of the molecules are in the main topology file, whereas the
> coordinates for the second molecule are read as .itp file
> (include file), or if both are read as include files, then there should
> be two position restraint files. If both molecules are built of
> building blocks (such as protein, DNA ...) then running separately
> pdb2gmx should generate adequate posre files for each of
> them. If one of the molecule is not built of standard building
> blocks (for instance, if it is a ligand, co-factor...) and
> you want nevertheless apply restraints to it in the simulation,
> then maybe the better solution is to write a short program
> (in C or FORTRAN) or script, which could filter out the
> numbering of non-hydrogen atoms.
> I hope it can help
> Best regards
> Paulo Netz
> Universidade Federal do Rio Grande do Sul
> Porto Alegre, Brazil
> On Wed, Oct 17, 2012 at 6:46 PM, Arman M. Soufiani
> <armansoufiani at gmail.com>wrote:
> > Dear Gromacs users,
> > It might seem a simple problem, however, I could not find a correct way
> > define two restrained groups in my .mdp file.
> > If I include the following an error appears that notifies me that I am
> > able to define two restraints!
> > define = -DPOSRES_1
> > define = -DPOSRES_2
> > Do I need to make an index for the collection of the atoms of both groups
> > and then use one define position restraint for them?!
> > If yes, I would be happy if you direct me how should I embed it in the
> > file?
> > Regards
> > Arman
> > --
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> > Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
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