AMBER Archive (2005)

Subject: AMBER: Trajectory problems

From: Steve Seibold (seibold_at_chemistry.msu.edu)
Date: Thu Mar 17 2005 - 13:21:37 CST


Dear Amber users
I am having trouble with my trajectory file (mdcrd). If I strip the
waters from the mdcrd file (which according to the output log goes ok)
and then attempt to measure rmsd, I get a message saying that while
processing AMBER trajectory file "Set #1 appears to be corrupted
(numbers....)" .
However, if I don't strip the waters from the file I have no problem
getting the rmsd.

My input for striping waters is :

Trajin protein.mdcrd.gz

Trajout protein_nowat.mdcrd

box 52.5 y 49.7 z 70.2
center :1-99 origin
image :100-198 origin center familiar
strip :WAT

go

My script for RMSd:

Trajin protein_nowat.mdcrd

box 52.5 y 49.7 z 70.2
center :1-99 origin
image :100-198 origin center familiar
 
rms first mass out file.txt time 5 :1-198_at_CA

I also checked the trajectory files before and after the removal of
water. Before I remove the waters the values are all positive, but after
water removal, many values are negative. It also makes no difference if
I remove the "box", "center" and "image" information. I still get an
error.

Can somebody give me some advice?

Thanks, Steve

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