AMBER Archive (2009)

Subject: [AMBER] ambmask question

From: Ed Pate (pate_at_math.wsu.edu)
Date: Mon Apr 06 2009 - 23:36:40 CDT

Dear Amber community:

I am trying to use ambmask to generate a file of atoms to be used as group
input in an amber md simulation. The group will be atoms outside a given
distance (22A) of an atom (5137) in the pdb file. The pdb file atom
numbering is generated by ptraj using the file.top and file.crd files.

My input command is

ambmask -p file.top -c file.crd -prnlev 1 -out amber -find "@5137 > :22"

The command generates the correct group. However, the output
numbers the group in RES format. The manual appears to indicate that ATOM
format can also be generated.

I am using Amber 8.

Can anyone help me to modify the ambmask command to generate ATOM format
in the ambmask output for the group input?

Thanks for the help.

Ed Pate

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