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.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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Received on Thu Mar 17 2005 - 19:53:00 PST
