[gmx-users] spliting chains

Erik Marklund erikm at xray.bmc.uu.se
Fri Mar 30 22:18:19 CEST 2007

30 mar 2007 kl. 22.00 skrev özge kül:

> Hi,
> Thank you for your advices.The A-chain is topologically similar to  
> the activation peptide of chymotrypsin(ogen) and connected in a  
> similar manner through the Cys1–Cys122 disulfide bridge to the B- 
> chain. Most of the A-B chain interactions involve charged side  
> chains; six are buried salt bridges, and 10 are involved in  
> interchain hydrogen bonds .In VMD I saw the two chains split up at  
> atime and then get together.I only know that I should  write -merge  
> in pdb2gmx line.According to the informations above how can you  
> help me?

I'd start by reading Tsjerk's and Andrea's answers again, and, more  
importantly, read up on the basics of MD. The latter piece of advice  
is motivated by the fact that covalent bonds CAN'T break in a  
classical MD simulation (with a few exceptions). Just as Andrea said,  
the topology needs to be checked to find out whether the disulfide- 
bonds are there or not.

Good luck.


> 1.      pdb2gmx_mpi -f 1ppbfree.pdb -p 1ppbfree.top -o   
> 1ppbfree.gro  -merge
> 2.editconf_mpi -f 1ppbfree.gro -o -d 0.8 -bt octahedron
> 3.      genbox_mpi -cp out.gro -cs -p 1ppbfree.top -o 1ppbfree-gen.gro
> 4.      grompp_mpi -v -f 1ppbfree-en.mdp -c 1ppbfree-gen.gro -o  
> 1ppbfree-en.tpr -p 1ppbfree.top
> 5.mdrun_mpi -v -s 1ppbfree-en.tpr -o 1ppbfree-en.trr -c 1ppbfree- 
> aftermin.gro -g 1ppbfree-en.log -e 1ppbfree-en.edr
> Bored stiff? Loosen up...
> Download and play hundreds of games for free on Yahoo! Games.
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before  
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20070330/f85835a0/attachment.html>

More information about the gromacs.org_gmx-users mailing list