Dear Brian,
> 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.
This is not a tricky 'use of RED': this is how was implemented the
default RESP charge fitting procedure to limit the number of
constraints and avoid too large increase of the RRMS value.
In general when a CH2 or CH3 group is involved in a constraint
(INTRA-MCC or INTER-MCC) the flag associated is often R for 'Remove';
in this case the charges of the atoms involved in the constraint are
frozen in the 2nd RESP fitting stage so not equivalenced; but the
corresponding atoms are removed ('R' flag) from the FF library because
not required for MD simulations; thus the problem of the absence of
charge equivalencing for CH2 and CH3 groups is avoided/hidden in this
case.
In your case you used the K (Keep) flag, this means you want to keep
the corresponding atoms in the FF lib for MD simulation; so the
charges are not equivalenced in the 2nd RESP stage. This is 'normal'...
Solution 1: repeat the constraint in the 2nd RESP input with an
additional degradation of the RRMS value; i.e. use INTRA-MCC2
implemented in R.E.D. Python (instead of INTRA-MCC1; i.e. INTRA-MCC in
R.E.D. Perl)
Solution 2: find another way to set up your fitting procedure using
R.E.D. Perl.
-> I do not understand why you want to constraint these 10 atoms to
the -0.2882 value - another approach should be possible...
regards, Francois
> 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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Received on Sat Aug 24 2013 - 09:00:05 PDT
