Dear George,
> I have created the parameters of a ligand with gaff setting the total
> charge to 0 (which is the default). When I load the generated mol2 into
> tleap and I issue
>
> charge lig
> I get
> Total unperturbed charge: -0.003001
>
> Is this a rounding issue or something?
I would answer that a rounding off error at 10-3 should have the
following shape:
0.000 +/-.00X
a rounding off error at 10-4 should have the following shape:
0.0000 +/-.000X
'3001' is strange - the answer is just I guess 'that is small'...
If you use R;E.D. Server or better now R.E.D. Server Dev./R.E.D.
Python there is not such an error; besides rounding off errors are
strictly corrected in agreement with chemical equivalencing & the
different charge constraints used during the charge fitting step.
See
http://q4md-forcefieldtools.org/REDS-Development/
& Concerning rounding off errors:
http://q4md-forcefieldtools.org/REDS-Development/Demo2-Files/Configuration.py
# Correct charge value rounding off errors at an accuracy defined by the user
# 6: correction at ± 1.10-6 e
# 5: correction at ± 1.10-5 e
# 4: correction at ± 1.10-4 e
# 3: correction at ± 1.10-3 e (pay attention)
# 2: correction at ± 1.10-2 e (pay a lot of attention)
# 1: correction at ± 1.10-1 e (do not use)
# 0: no correction is performed
# The default of COR_CHR = 4
COR_CHR = 4
Just submit your PDB file at
http://q4md-forcefieldtools.org/REDS-Development/ &
http://q4md-forcefieldtools.org/REDS-Development/upload-log.php
(without anything else; this is accepted by now) & compare...
regards, Francois
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Received on Wed Feb 12 2014 - 05:30:04 PST
