Thanks.
Lekpa.
On Wed, Mar 3, 2010 at 1:51 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Lekpa,
>
> Please, see . http://q4md-forcefieldtools.org/Help/Lekpa/ R.E.D. data, I
> quickly got with 3 models:
>
> [fyd.lynx Data-RED]$ grep "ESP relative" Mol_m?/output2*
> Mol_m1/output2_m1: ESP relative RMS 0.148
> Mol_m1/output2_m1.sm: ESP relative RMS 0.288 1.9x
> Mol_m2/output2_m2: ESP relative RMS 0.112
> Mol_m2/output2_m2.sm: ESP relative RMS 0.291 2.6x
> Mol_m3/output2_m3: ESP relative RMS 0.140
> Mol_m3/output2_m3.sm: ESP relative RMS 0.307 2.2x
>
> As you can see the best result - i.e. "the less worst" ;-) is obtained with
> the 1st model.
>
> Several comments:
> - a charge difference for a group of atom of .12 is quite common when using
> intra-mcc(s),
> - in your case, the "best" results found so far presents a charge
> difference of .16 which is slightly worst than this .12 value
> - may be better can be done, or you will have to live with this error
> considering that this is difficult to do better
> - you are now aware that the fit in this case is not that good & R.E.DD.B.
> presents several examples of charge fitting with more or less good RRMS
> values.
> Examples are Alkanes & CHCl3:
> http://q4md-forcefieldtools.org/REDDB/projects/W-42/
> http://q4md-forcefieldtools.org/REDDB/projects/W-43/
>
> regards, Francois
>
>
> PS if you want to send emails in the q4md-fft mailing list you need to
> register.
>
>
>
> 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
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>
>>> _______________________________________________
>>> 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
>>
>>
>>
>
>
> F.-Y. Dupradeau
> ---
> http://q4md-forcefieldtools.org/FyD/
>
>
>
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>
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Received on Wed Mar 03 2010 - 14:00:03 PST
