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.
/Erik
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@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 [EMAIL PROTECTED]
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
[EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys
_______________________________________________
gmx-users mailing list gmx-users@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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
