AMBER Archive (2008)

Subject: Re: AMBER: prmtop spec trivia

From: Lachele Foley (Lists) (
Date: Tue Apr 29 2008 - 13:25:53 CDT

Hi, Ross:

> The prmtop file description is in serious need of updating..., Feel free to
> volunteer...

By the time I'm done with this, it'll probably be very easy for me to
do that. I'll probably do something like it in the course of my usual
documentation. But, it might be a week or three before it'll be in a
form to show anyone else... If I do it, and I probably will, I'll
post to the developer list first for comments.

> Probably not although it would be nice if one did. Again perhaps some
> student with plenty of time on their hands could grep through the code and
> pull out all of the FLAGs that are expected.

Well... I don't know lots of students, and certainly none of the ones
around here would claim to have lots of time on their hands. But, a
grep is easy, provided the code isn't too twisty. I'll have to do it
to make sure my program is complete anyhow, but don't expect a
pretty-print list immediately.

> Although of course you'd need to modify
> the code itself if you wanted it to actually read the additional
> information.

Mine will read it, whatever it is, then catalog and store it. But,
it'll be up to the other functions to decide whether or not to use
it... If I had infinite time, I'd probably be programming the Star
Trek computer:

"unknown specifier 'electroneg_paul' found in topology file"
"speculate meaning and import"
"most probable meaning: Pauling electronegativities. generating array
space and saving data. shall I incorporate into current model?"


:-) Lachele
Lachele Foley
The AMBER Mail Reflector
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