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

Tsjerk Wassenaar tsjerkw at gmail.com
Thu May 24 22:44:50 CEST 2012

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 ;)



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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