Quoting Anthony Cruz <acb15885.uprm.edu>:
> Thank you for you rapidly responce. If you have time I want to ask you a
> question about the charge derivation. The chromophore was made from the
> cyclization of THR-TYR-GLY
> (http://pps.cryst.bbk.ac.uk/PPS2/projects/jonda/chromoph.htm). It have the
> side chains of the THR and GLY.
In your chromophore, you have a Thr instead of a Ser, if I understand you.
> During the charge derivation procedure could
> be good idea to do intra-molecular charge constraint in this sidechains or
> only on the N-H and C-O terminal atoms?
Sorry, I am not sure to understand you...
A good way to see if an intra-molecular charge constraint (INTRA-MCC)
can be applied in a RESP fit for a chemical group "X" is to do the fit
without this INTRA-MCC in a 1st step.
=> Then, compare the total charge value you get in the fit without the
INTRA-MCC for this chemical group "X" (i.e. manually calculate it) to
the value of the INTRA-MCC you wish to apply in a 2nd step/fit (for
this chemical group "X"). More the two values will be similar, better
will be your 2nd fit (i.e. the fit with the INTRA-MCC) & consequently
better will be your RRMS value.
Applying this, in two R.E.D. runs is straighforward:
Just add the INTRA-MCC keyword at the beginning of the line to run the
job with this INTRA-MCC, & add just a space character in front of the
INTRA-MCC keyword to run the job without this INTRA-MCC; i.e. in the
.p2n file, you do:
either
INTRA-MCC 0.0 | 1 2 etc... | K to run the fit without this INTRA-MCC
or
INTRA-MCC 0.0 | 1 2 etc... | K to run the fit with this INTRA-MCC
regards, Francois
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Received on Sun Jan 20 2008 - 06:07:06 PST
