AMBER Archive (2001)

Subject: Re: carnal error with crd files stripped of waters

From: samantha hughes (s.j.hughes_at_ic.ac.uk)
Date: Mon May 14 2001 - 03:20:17 CDT

Hi Michael,

What do you use to strip the waters ? Carnal or RDParm/PTRAJ ?

Samantha

Michael Cooney wrote:
>
> Dear AMBER users,
>
> When I run carnal to analyze distances/angles/torsions on a large mdcrd
> file, I like to strip the trajectory of waters in order to speed up the
> carnal run, but when I do this I get the following error at the end of my
> output file:
>
> allmdnowat.crd: too many numbers on box line for mdcrd format -
> bad coord file or carnal bug
>
> Has anyone else had this problem, and if so, is there an easy way to
> modify the stripped mdcrd file's box line so carnal will like it?
>
> Thanks very much for your help.
>
> Sincerely,
>
> Michael Cooney
> Dept. of Biochemistry and Molecular Biology
> The University of Georgia
> Athens, GA, USA