[gmx-users] Problem on processing proteins consisting of two chains

[David van der Spoel]

On Wed, 2003-11-26 at 07:05, wang chuanming wrote:
> Dear all,
>   I am a new user of Gromacs.I am trying to do a simulation on a protein 
> which consists of two chains(A and B) like HIV PR.Unfortunately, the two 
> chains got far away from each other. I found that two itp 
> files(protein_A.itp and protein_B.itp) were generated after using pdb2gmx. 
> It seems that Gromacs recognizes the two chains as different proteins,but 
> they belong to the same molecule indeed. 
Is there a covalent bond between the two?

You are probably seeing the result of periodic boundary conditions where
the two molecules seem to be separated, but aren't in reality.

>   How can I resolve the problem? Your experiences on Gromacs will helful 
> for me.
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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