AMBER Archive (2006)

Subject: AMBER: Problem with mask when using distance in ptraj

From: Christopher Gaughan (clgaughan68_at_gmail.com)
Date: Wed Nov 22 2006 - 13:36:23 CST

Dear all,

I was hoping someone could give me help with designating the mask for the
distance command in ptraj.
I am trying to measure the distance between two residues in separate alpha
helices over time. It seems like distance should work for this.

However, when I use the following input file:

trajin 1c1g_swammd.crd
trajout cgdimer_xanal nobox
distance ano out 1_distance1.dat time 0.1 @CA:244 @CA:544
strip :WAT
go

 I get an error message:

Mask [@CA:244] represents 0 atoms !!!NO ATOMS DETECTED!!!
Mask [@CA:544] represents 0 atoms !!!NO ATOMS DETECTED!!!
Segmentation fault

I have tried almost every combination and notation and just can't seem to
get this to work.
However, if I just use:

trajin 1c1g_swammd.crd
trajout cgdimer_xanal nobox
distance ano out 1_distance1.dat time 0.1 @CA:244
strip :WAT
go

This works, but I get a supiciously big output file.

I read all the archives on this subject but can't seem to fix this. Please
help

Chris

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