[AMBER] water mediated H-Bond

From: Sangita Kachhap <sangita.imtech.res.in>
Date: Tue, 1 Mar 2011 23:07:31 +0530 (IST)


I am doing water meadiated H-bond calculation.
What I did process mdcrd file using command:

trajin 1sa3_mono_NPT.mdcrd 1 600 1
closest 10 :115 first
trajout 1sa3_mono_NPT-close.mdcrd mdcrd

Also generate pdb file having 10 water molecule by taking one short from the
trajectroy using command:

trajin 1sa3_mono_NPT.mdcrd 1 600 400
trajout 1sa3_mono_NPT.rst restrt

Convert this to pdb file, modify pdb retain only 10 water and then use it to
generate new topology file in tleap.

When I use this topology file to visualize above processed trajectry file
structure was not proper there is some long bonds.

I am not getting where is mistake so please anybody suggest me.

With regard
Sangita Kachhap

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Received on Tue Mar 01 2011 - 10:00:04 PST
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