RE: [AMBER-Developers] SCEE and SCNB removed

From: Ross Walker <>
Date: Mon, 8 Feb 2010 23:30:57 -0800

Hi Lachele,

> I sent this around to the locals. They are thrilled that this is being
> worked on, but want to know why it isn't possible to do this:
> S -N -CG-H1 1 0.02 0.0 3. 1.2 2.0
> ***G06 - MT
> versus:
> S -N -CG-H1 1 0.02 0.0 3. ***G06 - MT
> S -N -CG-H1 1.2 2.0
> They think, perhaps erroneously, that the first method is "backwards
> compatible because any lines after 5th column are ignored." Is that
> not true? Are there other complications? They prefer having just the
> one line for simplicity's sake.

Indeed, Thomas Steinbrecher and I have been having the same discussion this
morning and I think this is probably the cleanest implementation. I.e. to
just include the SCEE and SCNB in columns 6 and 7 or the parmxx.dat file and
frcmod file. In this way older codes and parsers will just treat this as a
comment and it won't break anything. The only issue I see is that we don't
want to 'require' these values for the new code. I.e. we only really want to
update the glycam and weiner et al parm files, we want to leave all the
other parm and frcmod files untouched as they are now since they use the
defaults. The issue is making sure the new parser can identify when column 6
is a comment and when it is a scee + scnb value. This would be easy except
for the fact that there are comments such as "1989 value blah" so the first
entry in a comment can sometimes be a integer or float which could cause

I guess we could restrict the values of scee and scnb though, say between
0.5 and 2.5 so we would read the value and just see if what we got was in
this range and if it wasn't just ignore it and use the default values. I
think this would catch almost all comments. Obviously scee and scnb can
never be set to 0.0.

Lets wait and see what others comment and then we can formerly write up the
new file spec for this.

All the best

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | |

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Received on Tue Feb 09 2010 - 00:00:02 PST
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