[AMBER] stripWAT command and saving a new trajectory

From: Daniel Scott <dscott5.nd.edu>
Date: Mon, 10 Jan 2011 17:52:56 -0500

Hi AMBER users,
If I have a gzipped trajectory file, the following ptraj command writes a
new trajectory file (.mdcrd) without the water:

trajin A6WT_0_md_prod_1.mdcrd.gz
strip :WAT
trajout A6WTnoWAT.mdcrd nobox

Can I then calculate other ptraj commands (i.e., "dihedral," "analyze
timecorr," etc.) using these commands:

 trajin A6WTnoWAT.mdcrd
vector D26CO .365 corr @366
analyze timecorr vec1 D26CO tstep 200 tcorr 20000000.0 out D26COcorr.out

so that the time correlation function calculations are a lot faster? You
see, I have 100 of these .gz files, and it takes about 24hrs for a ptraj
calculation to run. I'm trying to save time by writing a new trajectory
file without the waters.

Thanks for any advice,
Daniel Scott
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Received on Mon Jan 10 2011 - 15:00:03 PST
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