najwa drici wrote:
hi all
I would like to extract my protein structure with the first hydration
shell around the active site which contains an ion from counfout.gro.
Is there any program script able to do this?
Not in one step, no. You could:
1. Use make_ndx to create an index group that defines your active site.
2. Use g_dist -dist to determine which water molecules (based on the atoms
listed) are within a defined distance from the active site residues.
3. Make another index group that contains protein + the waters identified in
step 2.
4. Extract those coordinates using trjconv and the index group created in step
3.
-Justin
Cordially DRICI nedjoua
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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 gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
