AMBER Archive (2006)

Subject: Re: AMBER: A script file for measuring the distance between 2 atoms during MD

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Wed Sep 27 2006 - 13:05:25 CDT

> I have the following script to measure the distance of
> the 67_at_OD1 and 110_at_NZ in a protein during MD. However
> when I run using $AMBERHOME/exe/ptraj *.prmtop <
> distance.in, it takes very long time and never ends
> for almost 1 hour thus I doubt there is something
> wrong. Will you please take a look and see what is
> wrong?
>
> ------------------------------
>
> trajin complex_md1.mdcrd
> distance DIST 67_at_OD1 110_at_NZ out 926MD1_distance.out
> strip :WAT
> go

ptraj prints out a lot of status information, and without this I cannot
determine what is going on. Also, you do not have the correct format for
the mask strings which should be :67_at_OD1 :110_at_NZ. I also do not see why
you need to strip the :WAT residues as this is irrelevent (since you are
not outputing a new trajectory or doing anything after the strip). I
highly recommend, *again*, to go through the tutorials...

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu