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

David van der Spoel spoel at xray.bmc.uu.se
Wed Nov 26 08:48:01 CET 2003

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.
> _________________________________________________________________
> 与联机的朋友进行交流,请使用 MSN Messenger:  http://messenger.msn.com/cn  
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
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

More information about the gromacs.org_gmx-users mailing list