[AMBER] Distance between two different solvent mask

From: MOHD HOMAIDUR RAHMAN <rahmanhpu.gmail.com>
Date: Mon, 16 Jul 2018 15:53:53 +0530

Dear Amber User

I want to calculate distance between two solvent mask closest to two end of
a protein. For that I have define two mask, solvent A that is near to resid
1 and solvent B near to resid 20. Here is my test cpptraj script I wrote
for calculating distance between A and B.

parm parm.parm7
trajin test.nc parm parm.parm7
trajin test2.nc parm parm.parm7
trajin test3.nc parm parm.parm7
solvent :A parm parm.parm7
closest 1 :1 closestout closestA.dat
trajout closestA.nc

solvent :B parm parm.parm7
closest 1 :20 closestout closestB.dat
trajout closestB.nc

distance ab :A :B out dist_ab.dat

Both solvent mask working individually and writing trajectory. But after
combining both together I am getting an error of no dataset during distance
calculation. After looking carefully I observe that solvent mask A is
getting replace by solvent mask B and I am getting trajectory of closest B

It is possible to work with two define solvent mask with closest command
and then calculate distance between them. I have TB of data, so I don't
want to rewrite trajectory every time it will take lot of disk space.
Thank you very much

*M*d* H*omaidur* R**ahman *( Research Scholar )
Lab No. 510, Computational Biophysics Lab.
Department of Biotechnology
Indian Institute of Technology-Madras
Chennai-600 036, India
*Mobile No = +91- 7845991785*
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Received on Mon Jul 16 2018 - 03:30:02 PDT
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