David van der Spoel wrote:
I work with a protein where 3 CYS redisidues make bond with a Zn atom by
its SG atoms and HIS redisidue makes bond with a Zn atom by its NE2 in
active site
I want to use deprotonated “cys”. In manual for “pdb2gmx “ clearly says
on option of choosing Cys protonated state possibility but why that
option not appearing while running “pdb2gmx” , just like for “Arg”,
“His”, “Asp” and “Glu”.
Without showing us your exact command line, we can only guess that you've not
given the correct command. Besides, the options for cysteine only apply to
protonated cysteine or the disulfide form in most conventional force fields;
these are the limitations of the force field.
Must i generate a specbond.dat entry for Cys-Zn His-Zn linkage ?
Yes. Consult the manual and wiki on how to do this.
And what type of histidine do I have to choose
0. H on ND1 only (HISA)
1. H on NE2 only (HISB)
2. H on ND1 and NE2 (HISH)
3. Coupled to Heme (HIS1)
That choice is yours based on structural/biophysical data available for your
protein.
-Justin
Best regards
Nedjoua Drici
------------------------------------------------------------------------
Discutez gratuitement avec vos amis en vidéo ! Téléchargez Messenger,
c'est gratuit ! <http://get.live.com/messenger/overview>
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
_______________________________________________
gmx-users mailing list [email protected]
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
