[gmx-users] Re: minimize multi-chain protein

[Florian Dommert]

On Jul 25, 2008, at 12:51 AM, amit.oberai at yale.edu wrote:

> HI,
>
> I am using gromacs for energy minimization.  Can anyone advise me on  
> how to do
> this for a multi-chain protein.
>
> When I try to minimize a protein with multiple chains, gromacs  
> creates a bond
> between the last residue of the previous chain and the first residue  
> of the
> next chain, not recognizing they are in separate chains.
>

If gromacs creates a bond between atoms, this bond is defined in the  
topology files.
So perhaps you are using itp - files that do not correspond to your  
system.

Best Regards

Flo

> My pdb file has distinct chain names for all the different chains.
>
> Thanks!
> Amit
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--
Florian Dommert
Dipl.-Phys.

Computational and Theoretical Softmatter & Biophysics group

Frankfurt Institute for Advanced Studies
Johann-Wolfgang-Goethe University

Ruth-Moufang-Str. 1
60438 Frankfurt am Main

Phone: +49(0)69 / 798 - 47522
Fax:   +49(0)69 / 798 - 47611

EMail: dommert at fias.uni-frankfurt.de
Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert

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