AMBER Archive (2008)

Subject: RE: AMBER: prmtop spec trivia

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Apr 29 2008 - 12:55:02 CDT

Hi Lachele,

> By extensible, do you mean that the FLAG and FORMAT lines will always
> appear and act as section delimiters/descriptors?

Yes the %FLAG and %FORMAT lines should always be there. The %FORMAT line
should be read by anything reading a prmtop file in order to obtain the
expected format for the field below. For example you could change:

%FLAG CHARGE
%FORMAT(5E16.8)

To be %FORMAT(4E20.10) if for some reason you wanted it stored in higher
precision in the prmtop file. I have not attempted to change the format
lines though so I don't know how compliant all of the various programs and
tools are.

As far as extensible goes what I mean is that you could specify your own
%FLAG XXX lines if you wanted without worrying about breaking other codes.
I.e. if you wanted to include some additional parameters you could do this
without breaking ptraj for example. Although of course you'd need to modify
the code itself if you wanted it to actually read the additional
information.
 
> By the way, I don't see these described on the prmtop file page:
>
> %FLAG RADIUS_SET
> %FLAG RADII
> %FLAG SCREEN
>
> Are there other common ones? Am I just being blind and those are
> somewhere in the description?

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

> And, I looked for a list of all the "FLAG" names, but didn't find one
> in the manual or the tools manual. Does one exist?

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.

Good luck,
Ross

/\
\/
|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk | PGP Key available on request |

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