Lekpa,
> 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.
- When adding intra-mcc(s) in a P2N file, R.E.D. automatically
generates two fits: one without this/these intra-mcc (useful as a
reference) with the corresponding files generated (among many others):
inputX_m1, outputX_m1, punchX_m1 (X = 1 or 2 so far), & the FF
library: Mol_m1-o1.mol2 and another one with the intra-mcc(s); files
generated: inputX_m1.sm, outputX_m1.sm, punchX_m1.sm & Mol_m1-o1-sm.mol2
See
http://q4md-forcefieldtools.org/Tutorial/P2N/Central-frag-Pept/listing-1mol.pdf
- (I suppose you use the RESP-A1 charge model) if I understand you, you got:
ESP relative RMS (SQRT(chipot/ssvpot)) 0.11363 in output2_m1
ESP relative RMS (SQRT(chipot/ssvpot)) 0.29321 in output2_m1.sm
If so, yes, this is bad. Surprising...
- What is the total charge (you have to compute it manually) of this
CH3CO group in the fit WITHOUT the intra-mcc (i.e. in Mol_m1-o1.mol2)
? if too different to zero this means that the CH3CO is not the right
group to be constrained and MeCO-OMe is not the right model (even if
the organic function is correct).
I will check that today. I let you know...
regards, Francois
> 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 02 2010 - 21:00:02 PST
