[gmx-users] BHIS for HIS?

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Apr 11 06:39:44 CEST 2007


Hi Rongliang Wu,

You could try to get your hands on a GROMOS manual... Alternatively,
draw the histidines using the information in the rtp files.
Alternatively, take a histidine, run it through pdb2gmx with -his and
try all options. Histidine has different protonation states, and one
of the histidines is the one bound to heme iron.

Cheers,

Tsjerk

On 4/11/07, Rongliang Wu <wurl04 at iccas.ac.cn> wrote:
> hello,gmx-users,
>         i am trying to simulate a peptide with residue HIS, the default in pdb2gmx used HISB for HIS in both oplsaa and gromos96 force field, but i found there are HIS1,HISH,HISB etc in the rtp files, i am not sure whether HISB will suffice for my system, i intend to simulate the binding of surfactants with the peptide.
>         what are the difference?
>         is there anywhere i can find the detailed description for these residues?
>
> Rongliang Wu
> wurl04 at iccas.ac.cn
> 2007-04-11
>
> _______________________________________________
> 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
>


-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623



More information about the gromacs.org_gmx-users mailing list