Francois,
Aha, that makes sense. The atoms intended to be equivalent are in fact two
methoxy groups. We can probably move this off list now that I know this is
a "tricky" use of RED.
Brian
On Fri, Aug 23, 2013 at 12:16 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Brian,
>
> > I am using RED-III.4 to derive charges for a molecule where some atoms
> are
> > chemically equivalent.
>
> better using the last version of the R.E.D. III.x tools; nowadays
> R.E.D. III.52
> & using R.E.D. Server/Ante_R.E.D. 2.0 instead of Ante_R.E.D. 1.x
> see http://q4md-forcefieldtools.org/REDS/news.php#2
>
> > I would also like to impose that the sum of certain
> > atoms have a fixed (non-zero) value.
>
> ok
>
> > The former is presumably accomplished by identical atom names in the p2n
> > file (although Ante_RED seems to change this from the input pdb, so I
> > changed it back "by hand") while the latter is done via a "INTRA-MCC"
> > remark in the input p2n:
> >
> > REMARK INTRA-MCC -0.2882 | 1 2 3 4 5 6 7 8 9 10 | K
>
> by default (as defined in Cieplak et al. JComputChem 1995
> http://www3.interscience.wiley.com/cgi-bin/abstract/109583237/ABSTRACT) an
> intra-mcc is only applied in the 1st RESP input and then the
> corresponding atoms have their charges frozen in the 2nd RESP stage
> (why? to limit the number of constraints and to not increase too much
> the RRMS value fo the fit). A tricky limitation of this approach is
> that if the intra-mcc contains CH2 and/or CH3 groups their charges
> will not be recomputed in the 2nd RESP stage and consequently not
> equivalenced. This limitation is solved in R.E.D. Python by providing
> two types of INTRA-MCC.
>
> > However, of the 4 output files (qout1_m1, qout1_m1.sm, qout2_m1, and
> > qout2_m1.sm) only one of them (qout2_m1) has equivalent charges imposed,
> > while all of the ".sm" files have the sum constraint imposed.
>
> the input1_m1 & input2_m1 correspond to the fit without intra-mcc
> -> should be correctly equivalenced
>
> the input1_m1.sm & input2_m1.sm correspond to the fit with intra-mcc
> -> CH2 & CH3 might not be equivalenced if included in an INTRA-MCC
>
> > Is there a different way to apply equivalencing constraints when also
> using
> > INTRA-MCC? Is this some "bug" from using an older version of RED?
>
> We can use R.E.D. Python & post-process your data until R.E.D. Python
> is available. Before proposing that could you please describe what are
> these "1 2 3 4 5 6 7 8 9 10" atoms?
> -> I bet there are CH2 & CH3 chemical groups ;-)
> If so only the new 'INTRA-MCC2' implemented in R.E.D. Python will
> solve your problem ('INTRA-MCC' in R.E.D. Perl becomes 'INTRA-MCC1').
>
> regards, Francois
>
>
>
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--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
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Received on Fri Aug 23 2013 - 09:30:03 PDT
