Dear Albert,
> I found that there is a problem in the output of my R.E.D program:
> there is no double in the mol2 file..... Since we may not assign the
> bond type in the PDB file, and I am wondering how can we deal with this
> problem?
A single, double or triple bond is only an empirical view. So, a
single, double or triple bond does not exist and is represented by a
different constant in a force field.
So far, we assigned force field atom types using a LEaP script: you
can find many examples in R.E.DD.B.
http://q4md-forcefieldtools.org/REDDB/projects/F-87/
http://q4md-forcefieldtools.org/REDDB/projects/F-87/script1.ff
http://q4md-forcefieldtools.org/REDDB/projects/W-46/
http://q4md-forcefieldtools.org/REDDB/projects/W-46/script1.ff
for instance:
# tripos8.mol2
set BNZ name "BNZ"
# head & tail not needed since whole molecule
# connect0 & connect1 not needed since whole molecule
set BNZ.1 restype solvent
set BNZ.1 name "BNZ"
# set FF atom types
set BNZ.1.C1 type CA
set BNZ.1.H1 type HA
set BNZ.1.C2 type CA
set BNZ.1.H2 type HA
set BNZ.1.C3 type CA
set BNZ.1.H3 type HA
set BNZ.1.C4 type CA
set BNZ.1.H4 type HA
set BNZ.1.C5 type CA
set BNZ.1.H5 type HA
set BNZ.1.C6 type CA
set BNZ.1.H6 type HA
# save the OFF library
saveoff BNZ BNZ.off
regards, Francois
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Received on Sun Feb 12 2012 - 00:30:06 PST
