Re: Problems with AMBER

From: John Finke <>
Date: Fri 29 Jun 2001 15:55:06 -0700 (PDT)

Thanks for the suggestion. Carnal is working out much better than ANAL.

I also have a question regarding carnal. I can specify residues but how do
you specify exact atoms when using the distance calculation DIST. (For
example, instructing the script to measure the distance between the
N-terminal Nitrogen atom and the C-terminal carboxyl carbon).


John Finke

On Thu, 28 Jun 2001, Bill Ross wrote:

> I'm trying to use the ANAL program to analyze output from an MD run. I
> have one major problem and one secondary question.
> My main problem is that my input crd file from MD contains data in 10
> columns. ANAL does not like this and won't accept it. However, it
> does seem to take my 6 column crd file which I obtained from
> minimization. Is there a flag I can use to get ANAL to accept
> the 10 column file format?
> No. The normal thing is to use carnal or some other program
> like ptraj to break out an mdcrd into a series of restrts,
> and then analyze each by way of a script. (Maybe Interface
> can help with this.) Also see the ANAL bugs on the 'Unfixed
> bugs' section of the amber web.
> Bill Ross
Received on Fri Jun 29 2001 - 15:55:06 PDT
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