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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Aug 23 2013 - 09:30:02 PDT
