Hi Ross,
Just want remind you that that sleap already handles 14 factor. currently it reads these factors from an extra section in the
frcmod file, and write the 14 factor section to topology file. See the test case under test/sleap/14scale for example. But it
should be fairly easy to modify the code so it should the format as you proposed.
Sincerely,
Wei
On Feb 9, 2010, at 10:33 PM, Lachele Foley wrote:
>> 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
>
> Got it. Would the extra line be in an entirely new section? That would probably be easier to do than than the way it looks in the example.
>
> Did you consider differentiating comments from values with some special characters, like (overkill here, perhaps):
>
> S -N -CG-H1 1 0.02 0.0 3. {SCEE/NB 1.2 2.0} ***G06 - MT
>
> It seems unlikely that anyone would have commented with such a set of characters. Also, the set could, theoretically, appear anywhere in the line, depending on how it gets written, e.g.:
>
> S -N -CG-H1 1 0.02 0.0 3. ***G06 - MT {SCEE/NB 1.2 2.0}
>
> ...not that one would necessarily have any reason to do that. I suppose it would make an easy way for other info to be added to other params in the future, if needed.
>
> :-) Lachele
> --
> B. Lachele Foley, PhD '92,'02
> Assistant Research Scientist
> Complex Carbohydrate Research Center, UGA
> 706-542-0263
> lfoley.ccrc.uga.edu
>
>
> ----- Original Message -----
> From: Ross Walker
> [mailto:ross.rosswalker.co.uk]
> To: 'AMBER Developers Mailing List'
> [mailto:amber-developers.ambermd.org]
> Sent: Tue, 09 Feb 2010 02:30:57
> -0500
> Subject: RE: [AMBER-Developers] SCEE and SCNB removed
>
>
>> 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
>> problems.
>>
>> 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
>> Ross
>>
>> /\
>> \/
>> |\oss Walker
>>
>> | Assistant Research Professor |
>> | San Diego Supercomputer Center |
>> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
>> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>>
>> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
>> be read every day, and should not be used for urgent or sensitive issues.
>>
>>
>>
>>
>>
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
_______________________________________________
AMBER-Developers mailing list
AMBER-Developers.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber-developers
Received on Tue Feb 09 2010 - 08:00:02 PST
