Алексей Раевский wrote:
Hi, I have got a situation and I don't know how to cope with it. I
carried out a simulation in gromacs 4.5.3 and the objects are protein,
rna, water...The idea is that one atom part of rna has to create an
h-bond with a water molecule, which at the same time makes h-bonds with
aminoacids of the binding site. Something like a coordination molecule.
So a command g_dist with index file and distance 0.35 showed me a number
of water molecule I needed. But when I decided to visualize this process
I saw that my protein with rna went out from the water box to another
"cell" and the part of rna sppeared in the bottom of this box (( as I
know this is not a bug or error of pbc. But i don't understand what is
happening. Does my water forms bonds with this part and aminoacids (!!!)
of binding site, because when I've converted trr to pdb with index file
(atoms of binding site, part of rna, water molecules I've got with
g_dist) I saw water molecules with part of rna in the bottom of display
and binding site in the top...I tried to use -pbc nojump and center,
-pbc mol...this flags united protein, rna and part of rna togetrher, but
my water is not there (((( Thank you
For proper visualization, there is a workflow here:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
For complex systems, multiple iterations of trjconv are almost certainly
required, some or all of which might need custom index groups.
Bridging and simultaneous hydrogen bonds have been discussed frequently in the
last few weeks. Have a look through the list archive. g_dist and g_hbond are
the proper tools, but multiple operations and your own post-processing of such
data will be required to extract the information you need.
-Justin
--
========================================
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
