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
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Received on Wed Mar 03 2010 - 13:00:05 PST
