[gmx-users] (no subject)

Алексей Раевский rayevsky85 at gmail.com
Tue Mar 15 23:36:48 CET 2011

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
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