[gmx-users] MD for two merged chains

[Tsjerk Wassenaar]

Hi Dimitry,

Well, you can use pdb2gmx with -merge to merge chains.

Hope it helps,

Tsjerk

On Mon, Sep 22, 2008 at 4:12 PM, DimitryASuplatov <genesup at gmail.com> wrote:
> Hello,
> I have a two-chain protein. I want to merge N-terminal residue of chain
> A with C-terminal of chain B. I can tweak the coordinates with pymol but
> when I run energy minimization two chains split again because gromacs
> fairly treats the input as a two-chain protein.
> I could switch the ATOM entries for chains A and B in the coordinate
> file - so that they are in the right order - and then delete the chain
> identifier, this workout will not help in more complex situations like 4
> chains merge though.
> Is there any option that allows gromacs not to consider chain IDs and
> the order of aa in the coordinate?
> Thanks. I really appreciate your help.
> SDA
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
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