I am using RED-III.4 to derive charges for a molecule where some atoms are
chemically equivalent. I would also like to impose that the sum of certain
atoms have a fixed (non-zero) value.
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
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.
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?
Thanks,
Brian
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
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address.
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Received on Fri Aug 23 2013 - 08:30:03 PDT
