Thanks Francois. I indeed need an OMe for an ester group. I will try to
follow your suggestions.
Lekpa
On Tue, Mar 2, 2010 at 3:29 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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 - 07:30:03 PST
