Hello all
I have a trajectory of 2ns and by using VMD script I have found total 10 water
molecules exist
between the mask atom,with change in frame, water molecule number(position
number in pdb)is changing.
When I visualized the trajectory by selecting those of 10 water moleclues,water
moleclue 3701 is residing for 1-80ps 5445 82-115ps and so on.
Now I have to do MMPBSA and for this I have to strip all water moleclues except
10 selected.
I am using following command:
trajin prod-1-image.mdcrd 1 2000 1
strip
:105-114,116-475,477-2771,2773-2832,2834-2967,2969-3700,3702-3703,3705-4186,4188-4627,4629-5766
trajout prod-1-image.mdcrd mdcrd
But this script stripping only upto 5749 not upto last number 5766.
Is there any limitation for stripping total number of molecules?
Is there renumbring of position of water moleclue in processed mdcrd file after
striping of them?
Can anybody please make it clear for me?
With regard
Sangita Kachhap
JRF
BIC,IMTECH
CHANDIGARH
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Received on Fri May 27 2011 - 00:30:02 PDT
