Dear Jason and Marc,
>> 2) If not, would a 'simple' solution, in which I'd just add the atoms in
>> analogy to GLU and then manually change the charges similarly to the
>> changes between GLU in amino12.in and aminoct12.in, be OK? Or would
>> redeveloping the charges (e.g. with RED) be the only appropriate solution?
>
> My approach (and others may disagree here) is that if the changes you would
> make by hand are fairly small, there's probably not much need to re-derive
> charges. If the charge differences are large, then rederiving may be an
> appropriate option, although you'll have to take care to apply
> 'appropriate' charge constraints for consistency. (hopefully hand-editing
> will work).
I would re-compute the charge values for three main reasons:
- the differences in charge values for a molecule can be important
when one compares an anion/carboxylate and a neutral molecule/carb.
acid.
- the optimized geometry for an anion and a neutral molecule are
generally different
- finally the charge derivation procedure itself can be different;
i.e. for neutral terminal fragment one might not adopt an approach
involving 2 building blocks.
regards, Francois
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jun 02 2012 - 23:30:02 PDT
