Hello Francois,
I have submitted the ligand to the RED server. Are the calculated charges
in the force field library file Mol-sm_m1-c1.mol2, in 9th column? If yes,
they are quite different than AM1-BCC ones I got with AmberTools.
I will re-run antechamber providing the charges calculated by RED
George
> 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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Dr. George Patargias
Postdoctoral Research Fellow
Biomedical Research Foundation
Academy of Athens
4, Soranou Ephessiou
115 27
Athens
Greece
Office: +302106597568
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Received on Wed Feb 12 2014 - 10:00:02 PST
