Dear George,
> 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?
Let's take an example - the mol3 file generated at:
http://cluster.q4md-forcefieldtools.org/~x/Project/P10708.html
x = your cluster account (hidden)
head -n 14 Mol-sm_m1-c1.mol2
#
# Generated by R.E.D. Python version NOV-2013
#
http://q4md-forcefieldtools.org
#
.<TRIPOS>MOLECULE
CKH
39 41 1 0 1
SMALL
USER_CHARGES
.<TRIPOS>ATOM
1 CAQ 0.314821 -0.308671 2.528001 CT 1 CKH -0.1785 0.8780 ****
2 H1 0.678281 -0.454027 3.541891 HC 1 CKH 0.0793 0.1350 ****
3 H2 -0.337581 -1.144493 2.289118 HC 1 CKH 0.0793 0.1350 ****
4 H3 -0.281444 0.592544 2.511604 HC 1 CKH 0.0793 0.1350 ****
Yes, charge values are in the 9th column - you can compare the values
with these available in the RESP output. The 10th column is about
polarizability values required for the non-additive force field model
(you do not need that).
This mol3 file format (vs mol2) is described at:
http://q4md-forcefieldtools.org/Tutorial/leap-mol3.php
(we have to describe the update of the mol3 file format concerning
pol. values)
vs
http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php
> If yes,
> they are quite different than AM1-BCC ones I got with AmberTools.
Well, this is a known problem-feature - this has been discussed
several times in the Amber & q4md-fft mailing lists.
See
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/
Charge values based on MEP depend on conformation and for a given
conformation on molecular orientation - only using R.E.D. & by
controlling the mol. orientation for a well defined conformation leads
to reproducible charge values.
Concerning AM1-BCC they are designed to reproduce MEP - so this is
_not_ surprising they are different from RESP charges. I do not use a
method 2 (AM1-BCC) that performs approximation compared to a method 1
(RESP), that costs almost nothing nowadays from a cpu point of view...
Approximation is useful, only when something costs something (just my
personal opinion)...
> I will re-run antechamber providing the charges calculated by RED
R.E.D. Server Dev./R.E.D. Python performs atom typing, frcmod & leaprc
file generation - besides charge derivation and force field library
building.
See
http://q4md-forcefieldtools.org/REDS-Development/news.php
vs
http://q4md-forcefieldtools.org/REDS/news.php
In your case R.E.D. Python allows generating a force field for your molecule:
See the graphical interface of the project P10708:
Force field parameters and LEaP script
No File(s) Download
1 frcmod.correspondence
2 frcmod.known
3 frcmod.unknown
4 leaprc.ff13q4mdfft
- look at the frcmod.known & frcmod.correspondence files for known FF
parameters.
- look at frcmod.unknown to study FF parameters that you need to think about:
You can build your own frcmod.user file to provide to R.E.D. Python
missing FF parameters found in frcmod.unknown; here you control the FF
(missing or even known) you need (FF parameters in frcmod.user
overwrite others if duplicate are found):
See
http://cluster.q4md-forcefieldtools.org/~x/Project/P10708/Data-R.E.D.Server/Data-Default-Proj/frcmod.unknown
Set Re_Fit = "On" in Configuration.py
provide a new archive file that contains:
See
http://q4md-forcefieldtools.org/REDS-Development/popup/poparchive.php
- your frcmod.user file
- your Configuration.py file
- your Project.config file (if needed)
- your previous R.E.D. Python job
Create the archive:
tar cvf Arch.tar frcmod.user Config*.py Proj*.config Mol_red*
Data-R.E.D.Server
Compress it to upload it more easily:
bzip2 -9 Arch.tar
At the end you just run the leaprc.ff13q4mdfft fil generated by R.E.D. Python:
xleap -f leaprc.ff13q4mdfft
http://q4md-forcefieldtools.org/REDS-Development/images/RED-Python.gif
You can slightly adapt this leaprc.ff13q4mdfft file to add frcmod file
for tip3p water molecules, load new lib (solvent.lib), create alias if
needed etc... and finally generate your prmtop/prmcrd files.
I hope this helps...
regards, Francois
>> 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 - 22:30:04 PST
