Hello Francois
Using RED as you suggested, the the derivation was carried out but it
appears that the constraint really reduced the accuracy of the fit from a
value of 0.11363 to 0.29321. Since I do not have a lot of experience with
charge derivation in this manner I am not particularly sure if this is an
acceptable number. I suppose I will try other compounds to see if I get a
better fit. Any thoughts welcome! Thanks. Lekpa.
On Tue, Mar 2, 2010 at 8:03 AM, Lekpa Duukori <duukori.gmail.com> wrote:
> 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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>>
>
>
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Received on Tue Mar 02 2010 - 19:00:02 PST
