The result is even worse for EtCO-OMe, RRMS 0.36273 versus 0.13222.
If one is going to simulate a peptoid such as the case I have in which the
amno acid is capped by ACE and OMe, I would think that doing a charge
derivation where just backbone atoms are constrained to original amber
charges should be be sufficient ?
I am asking because when I do this I get much better RRMS values after a two
stage fit with constraints at the first stage to all_amino94.in charges on
backbone ( CA,N,C,O) atoms and fixing these along with some other heavy
atoms at the second stage. I get RRMS valus of 0.13718 v 0.09571 at the
first stage.
I had tried to fix the charges on ACE atoms to amber charges but somehow the
resp program does not effect this constraint.
Thoughts welcome!
Lekpa
On Tue, Mar 2, 2010 at 10:58 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Lekpa,
>
>
> 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.
>>
>
> ok, so this is normal that the RMSD of the fit with this intra-mcc is not
> that good. Now, what about EtCO-OMe ? Does it improve the fit & does it at
> least go in the right direction ?
>
> Corresponding P2N input file:
>
> REMARK INTRA-MCC 0.0 | 1 2 3 4 5 6 7 8 9 | Remove
> REMARK
> ATOM 1 C1 EST 1 X.XXX Y.YYY Z.ZZZ CX
> ATOM 2 H11 EST HX1
> ATOM 3 H12 EST HX2
> ATOM 4 H13 EST HX3
> ATOM 5 C2 EST CY
> ATOM 6 H21 EST HY1
> ATOM 7 H22 EST HY1
> ATOM 8 C3 EST CZ
> ATOM 9 O4 EST OZ
> ATOM 10 O5 EST O1
> ATOM 11 CT6 EST C1
> ATOM 12 H6 EST H11
> ATOM 13 H6 EST H12
> ATOM 14 H6 EST H13
>
>
> regards, Francois
>
>
> 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
>>>>>>
>>>>>
>
>
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Received on Wed Mar 03 2010 - 10:30:05 PST
