[gmx-users] Re: One molculetype for 3 proteins

[Steven Neumann]

Tahnk you both. Indeed, it works so -chainsep interactive

Steven

On Thu, May 24, 2012 at 9:44 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Okay,okay, I give in. To settle this again, I looked it up, and among
> the options to -chainsep is 'interactive'. If you use that you're
> prompted whether or not to separate at the breaks pdb2gmx detects.
> That allows you to merge chains. I guess there'd be sense in just
> having an option 'no' to merge everything, but that's for the
> developers to pick up ;)
>
> Cheers,
>
> Tsjerk
>
> On Thu, May 24, 2012 at 10:28 PM, Francesca
> <francesca.stanzione at unina.it> wrote:
> > I had the same problem and I didn't  find any way to do it. So i created
> new
> > residues for the terminals, and I added them to the forcefields files.
> > Example: if my first COOH terminal was a SER i created a SERT residues
> and I
> > used the COOH values taken from ASP , and the same procedure was used for
> > the next Nterminal...in that way I have a SERT in the list of amminoacids
> > and when you process the pdb2gmx you have 1moleculetype, but you have 3
> > different chains each with its terminals.  Be careful to use correct
> values
> > and add these residues to the list of amminoacids in the forcefield
> > directory. I used that method and I could apply the distance restraints.
> >
> > Cheers,
> > Francesca
> >
> > --
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>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
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