AMBER Archive (2005)

Subject: Re: AMBER: Trajectory problems

From: Melinda Layten (mlayten_at_gmail.com)
Date: Thu Mar 17 2005 - 13:34:50 CST

Do you feed in a different topology and coordinate file to reflect the
now stripped trajectory?

Melinda Layten

On Thu, 17 Mar 2005 14:21:37 -0500, Steve Seibold
<seibold_at_chemistry.msu.edu> wrote:
>
>
> 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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