Hello
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
JRF
BIC,IMTECH
CHANDIGARH
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Received on Tue Mar 01 2011 - 10:00:04 PST
