Dear Lekpa,
> Please does anyone know if there is an OMe fragment in the AMBER FF
> parameters? I want to do an OMe cap instread of the usial NMe
>
> I cannot find one, just checking to see if I somehow missed it.
>
> In the case that it does not exist, is the usual parm94 method the right way
> to go about making charges for this?
If I well understood your problem, you need an OME fragment
representative of an _ester_ group:
I do not think you can use the "OME" fragment available in the GLYCAM
force field topology database (FFTopDB) (because the corresponding
charge derivation has been carried out using the CHELPG algo. & this
fragment has been designed to cap an _acetal_) and you cannot use the
"NME" or "ACE" fragments available in the AMBER FFTopDB because they
were designed to cap a peptide with two _peptide bonds_.
However, you could follow a similar approach to that used to generate
the NME or ACE chemical group or for the central fragment of an
amino-acid:
See for instance:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
You need to define an "intra-molecular charge constraint" (intra-mcc)
set to zero for a chemical group you are going to remove, while you
are going to keep the OME group. The definition of an "intra-mcc" is
available in the section "-7th area-" in the resp manual.
See
http://q4md-forcefieldtools.org/RED/resp/ &
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#10
The key point is to find the right molecule where you will apply this
intra-mcc. You might start from an ester such as MeCO-OMe where you
are going to define an intra-mcc set to zero for the acetyl group
(MeCO); thus the total charge of your OME fragment will be an integer
(zero) i.e. compatible with the Amber FFTopDB.
If you decide to use the R.E.D. tools, this approach is
straightforward: you only need to use the INTRA-MCC keyword in a P2N
input file for the selected group of atoms involved in the constraint
such as:
REMARK INTRA-MCC 0.0 | 1 2 3 4 5 6 | Remove
=> set the intra-mcc to zero &
remove the atoms numbers 1-6 (CH3CO group) from the FF library
(mol2 file format)
REMARK
REMARK TITLE Ester...
REMARK CHARGE-VALUE 0
REMARK MULTIPLICITY-VALUE 1
REMARK INTRA-MCC 0.0 | 1 2 3 4 5 6 | Remove
REMARK
ATOM 1 C1 EST 1 7.137 -3.656 0.065 C1
ATOM 2 H11 EST 1 7.203 -4.172 -0.893 H11
ATOM 3 H12 EST 1 7.873 -2.853 0.099 H12
ATOM 4 H13 EST 1 7.333 -4.369 0.866 H13
ATOM 5 C2 EST 1 5.738 -3.078 0.230 C2
ATOM 6 O3 EST 1 5.589 -1.896 0.530 O3
ATOM 7 O4 EST 1 4.754 -3.918 -0.044 O4
ATOM 8 CT5 EST 1 3.441 -3.409 0.022 C5
ATOM 9 H5 EST 1 3.250 -3.022 1.023 H51
ATOM 10 H5 EST 1 2.731 -4.206 -0.202 H52
ATOM 11 H5 EST 1 3.326 -2.605 -0.706 H53
CONECT 1 2 3 4 5
CONECT 2 1
CONECT 3 1
CONECT 4 1
CONECT 5 1 6 7
CONECT 6 5
CONECT 7 5 8
CONECT 8 7 9 10 11
CONECT 9 8
CONECT 10 8
CONECT 11 8
END
You run R.E.D.-III.x & you directly get a Tripos mol2 file fragment
for OME in the organic function you are interested in.
Finally, the key is to look at the RRMS of the fit & check if the
"intra-mcc" used does not break the fit; in this case, R.E.D.
automatically fits with & without the intra-mcc; thus, you can easily
compare both fits.
Anyway, this MeCO-OMe model should provide you a reasonable starting point.
regards, Francois
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Received on Tue Mar 02 2010 - 02:30:02 PST
