Dear Chetna, dear Paul,
As Dr Case wrote two enantiomers have the same atomic charges, although :-)
If you are not aware of some 'potential' problems [2 different
molecular orientations before MEP computation for the 2 optimized
enantiomers (quite usual for different QM programs); different
conformations for the 2 optimized enantiomers (quite usual error),
bad_? accuracies for the optimized enantiomer geometries] you will end
up with different charge sets for two enantiomers.
Your best bet to derive _identical_ charges for 2 enantiomers is to
construct one enantiomer, and then define the second one as the image
of the first one (i.e. by replacing x by -x in a text editor).
I ran a test for you using PyRED using 2-butanol (R vs S)
(based on
http://q4md-forcefieldtools.org/REDServer-Development/faq.php#20):
See
http://q4mdfft:q4mdfft2012.cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFOmADFP3sbUADFh6PZnMFAiRXhN9I77boZa0/P3956.html
(data available 5 days)
The two PDB inputs:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFOmADFP3sbUADFh6PZnMFAiRXhN9I77boZa0/P3956/Mol_red1.pdb (x, y,
z)
vs
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFOmADFP3sbUADFh6PZnMFAiRXhN9I77boZa0/P3956/Mol_red2.pdb (-x, y,
z)
As you can see the charge sets are identical:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFOmADFP3sbUADFh6PZnMFAiRXhN9I77boZa0/P3956/Applet-dir_P3956/javascript_applet-mol2-3.html
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFOmADFP3sbUADFh6PZnMFAiRXhN9I77boZa0/P3956/Applet-dir_P3956/javascript_applet-mol2-4.html
in two different FF libraries:
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFOmADFP3sbUADFh6PZnMFAiRXhN9I77boZa0/P3956/Data-R.E.D.Server/Mol_MM/Mol_mm1-c1.mol2
(y)
.<TRIPOS>ATOM
1 C1 -1.853784 -0.034078 0.475481 CT 1 SBT -0.3056 0.0000 ****
2 H11 -2.111047 0.834071 1.074103 HC 1 SBT 0.0720 0.0000 ****
3 H12 -2.632866 -0.186601 -0.262899 HC 1 SBT 0.0720 0.0000 ****
4 H13 -1.839094 -0.899239 1.135382 HC 1 SBT 0.0720 0.0000 ****
5 C2 -0.504655 0.147421 -0.211765 CT 1 SBT 0.3303 0.0000 ****
6 H2 -0.557386 1.013189 -0.862395 H1 1 SBT 0.0675 0.0000 ****
7 O2 -0.239219 -0.930352 -1.080899 OH 1 SBT -0.6980 0.0000 ****
8 H22 -0.210844 -1.735175 -0.580105 HO 1 SBT 0.4313 0.0000 ****
9 C3 0.635273 0.352561 0.786457 CT 1 SBT -0.0716 0.0000 ****
10 H31 0.710125 -0.532232 1.418976 HC 1 SBT 0.0176 0.0000 ****
11 H32 0.378075 1.177192 1.446988 HC 1 SBT 0.0176 0.0000 ****
12 C4 1.982417 0.625764 0.120100 CT 1 SBT -0.0576 0.0000 ****
13 H41 2.262575 -0.186352 -0.539805 HC 1 SBT 0.0175 0.0000 ****
14 H42 2.765098 0.746680 0.862592 HC 1 SBT 0.0175 0.0000 ****
15 H43 1.945070 1.535513 -0.472430 HC 1 SBT 0.0175 0.0000 ****
http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFOmADFP3sbUADFh6PZnMFAiRXhN9I77boZa0/P3956/Data-R.E.D.Server/Mol_MM/Mol_mm2-c1.mol2
(-y)
.<TRIPOS>ATOM
1 C1 -1.853784 0.034078 0.475481 CT 1 RBT -0.3056 0.0000 ****
2 H11 -2.111047 -0.834071 1.074103 HC 1 RBT 0.0720 0.0000 ****
3 H12 -2.632866 0.186601 -0.262899 HC 1 RBT 0.0720 0.0000 ****
4 H13 -1.839094 0.899239 1.135382 HC 1 RBT 0.0720 0.0000 ****
5 C2 -0.504655 -0.147421 -0.211765 CT 1 RBT 0.3303 0.0000 ****
6 H2 -0.557386 -1.013189 -0.862395 H1 1 RBT 0.0675 0.0000 ****
7 O2 -0.239219 0.930352 -1.080899 OH 1 RBT -0.6980 0.0000 ****
8 H22 -0.210844 1.735175 -0.580105 HO 1 RBT 0.4313 0.0000 ****
9 C3 0.635273 -0.352561 0.786457 CT 1 RBT -0.0716 0.0000 ****
10 H31 0.710125 0.532232 1.418976 HC 1 RBT 0.0176 0.0000 ****
11 H32 0.378075 -1.177192 1.446988 HC 1 RBT 0.0176 0.0000 ****
12 C4 1.982417 -0.625764 0.120100 CT 1 RBT -0.0576 0.0000 ****
13 H41 2.262575 0.186352 -0.539805 HC 1 RBT 0.0175 0.0000 ****
14 H42 2.765098 -0.746680 0.862592 HC 1 RBT 0.0175 0.0000 ****
15 H43 1.945070 -1.535513 -0.472430 HC 1 RBT 0.0175 0.0000 ****
However adding a D-aminoacid 'in the middle' of L-aminoacids (within
an oligopeptide) is a different story: this is NOT an enantiomer
related problem; this leads to diastereosiomers, which for sure share
different atomic charge sets: this can be easily checked by deriving
charges for a LL-diaminoacid vs a DL-diaminoacid (or better_? a
LLL-triaminoacid vs a LDL-triaminoacid). This was discussed at least
twice in the Amber mailing list in the past (with Dr Simmerling).
I hope this helps,
regards, Francois
> For this, I first created an Isovaline residue (using Marwinsketch or any
> other chemical molecule editor) and changed its chirality using Avogadro.
> These molecules then can be used as input to the R.E.D server for charge
> calculation and force field parameters.
>
> http://upjv.q4md-forcefieldtools.org/REDServer-Development/
> go through their many tutorials on how to create such entities.
> On Sat, Mar 31, 2018 at 7:05 AM, <rabi1993.iitg.ernet.in> wrote:
>
>> I want to work on chirality sensing of epoxides. But I have no idea how
>> to create structures and force field parameters for these 'R' and 'S'
>> enantiomers separately. Is there any tools for creating these types of
>> structure and force field?
F.-Y. Dupradeau
---
http://q4md-forcefieldtools.org/FyD/
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Received on Wed Apr 04 2018 - 02:00:03 PDT
