Hi Oliver, Bill, Case and
Jason
very thanks for your time and
attention.
Dear
Case
>Are the coordinates of some water molecule in the amber trajectory file
different than those from gromacs?
How can I determine coordinates of some water molecule in the amber and
gromacs trajectory files?
>If you don't want those
bonds,
I need to water molecules perfectly and exactly as H-O-H. I want to do water
mediated hydrogen bond analysis.
Dear
Jason
>Are the lengthened O-H bonds present in your PDB that you use to create
your prmtop file?
No. in my PDB that I use to creat my prmtop file, O-H bonds and water
molecules are normal.
Dear
Bill
> What is the length of the OW-HW
bond?
length of the OW-HW bond relating to a special water molecule in a certain
time is 4.9 nm and 0.1 nm
in amber and gromacs, respectively.I calculated these distances by g_bond in
gromacs and ptraj (distance) in amber.
> and what do you
expect?
I want to know, despite these conditions about water molecules, is doing of
some analysis with ptraj (water mediated hydrogen bond) correct.
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
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Received on Mon Dec 27 2010 - 01:30:01 PST
