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

[Tsjerk Wassenaar]

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
>
> --
> View this message in context: http://gromacs.5086.n6.nabble.com/One-molculetype-for-3-proteins-tp4997727p4997736.html
> Sent from the GROMACS Users Forum mailing list archive at Nabble.com.
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists



-- 
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