You are right I used the RESP-A1 model and the RRMS results you quote are
true. The charge in the Mol_m1-o1.mol2 file for the CH3CO fragment is about
0.2 which is indeed quite different from zero. Also the charge on the OMe
oxygen is quite defferent between constrained and non constrained fit:
-0.4435 for unconstrained agaist -0.1909. Even the hydrogens are also too
different, 0.0819 and 0.1075 respectively. It seems as if the may not be the
right constraints and or molecule.
Lekpa.
On Tue, Mar 2, 2010 at 9:44 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 02 2010 - 21:30:09 PST
