AMBER Archive (2008)

Subject: AMBER: Water tracking

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Fri May 02 2008 - 10:09:35 CDT

Hi AMBER

I emailed yesterday about tracking a water molecule. I have created
water trajectories using "closest" ("closest 3 :557_at_NH1 oxygen") command
in ptraj. This seems to work fine. I get a mdcrd output of the
trajectories. However, when I try to measure the distance between
residue 557_at_NH1 to the first water oxygen over the trajectories I get
this error: "./ptraj Memory fault".

 

My input is as follows:

 

Trajin File.mdcrd

 

Distance one time 5 :557_at_NH1 :1_at_O file.txt

 

Go

 

My output seems to be ok down to "processing AMBER trajectories file X

 

Set.............."

 

And then I get the error ."/ptraj Memory fault" There is no dumping of
data.

 

I talked to our computer analyst and he informed me that it must be an
AMBER problem.

 

Can someone help me on this?

 

 

Thanks, Steve

 

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