The charges from all_prot_nucleic10.lib come from RESP calculations using
HF 6-31G*, if I recall correctly. Inter-molecular constraints were used to
keep the charge of the sugar ring equal to the corresponding base with the
normal protonation state, so only the charge on the bases changed.
HTH,
Jason
On Wed, Jul 4, 2012 at 4:16 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> Dear Asmita,
>
> I do not know where come from the charge values available in
> all_prot_nucleic10.lib, and I cannot answer instead of the Amber
> developers... You should send this type of query in the Amber mailing list,
> and not to my personal email address.
>
> That being said a related problem (I guess) has been discussed many times
> in the Amber mailing list, and a summary of the causes of this problem is
> available (I guess) in the R.E.D. tools article.
> See http://www.ncbi.nlm.nih.gov/**pmc/articles/PMC2918240/<http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/>
> See http://www.ncbi.nlm.nih.gov/**pmc/articles/PMC2918240/#**S7title<http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2918240/#S7title>
> See the section: "Charge reproducibility"
>
> To try to make the answer short, conformation 'greatly' (not defined)
> affect charge values; and molecular orientation '' affect charge values
> (all that is rather vague...). This means that even if a well defined
> conformation is involved in charge derivation two users are likely to
> generate two different sets of charge values when using the GAMESS, Firefly
> and Gaussian programs ... or even using only Gaussian. Thus, I would answer
> that the charge values in all_prot_nucleic10.lib (but once again I have no
> idea where they come from) are not reproducible simply because one has no
> information (i) about the conformation(s) involved in charge derivation,
> and (ii) the molecular orientation(s) is(are) unknown as well... The type
> of grid of points/surface(s) involved in MEP computation has also to be
> rigorously defined.
>
> This is why R.E.D., R.E.DD.B. and by now R.E.D. Server have been
> developed. By rigorously controlling all the parameters that affect
> non-polarizable MEP-based charge values in R.E.D. and by reporting these
> parameters in R.E.DD.B. the charge values are reproducible by other users.
> Thus, by using R.E.D. you will not be able to reproduce the charge values
> available in all_prot_nucleic10.lib (my guess), but other users will be
> able to reproduce the data you generate.
>
> As a test you can take data from R.E.DD.B. and try to reproduce the
> corresponding charge values; then, apply the same strategy to reproduce
> charge values in all_prot_nucleic10.lib.
>
> I hope this helps.
>
> regards, Francois
>
>
> I am having a confusion here regarding library file for protonated nucleic
>> acid bases. What is the QM scheme used in Amber11/12 to generate partial
>> charge values for protonated bases in all_prot_nucleic10.lib file given
>> with amber12.
>>
>> To say it more clearly, why partial charge values for an N3 protonated
>> cytosine using Gaussian09 and RED server(generated by me) are different
>> from that given in all_prot_nucleic10.lib file. The 2 residues are same.
>> I
>> have used HF/6-31G for Gaussian geometry optimization followed by RED
>> calculation.
>>
>> Does that mean that Amber uses a different scheme for calculation of these
>> values. Also, these files have been added in the recent versions of amber.
>> They were not present in Amber9. I am in a fix here as to which values to
>> be used for further MD simulation.
>>
>> Here i am giving partial charge values in the two cases:
>>
>> N3-protonated cytosine :
>>
>> Amber12 values RED values
>>
>> N1: 0.1954 0.0520
>> C2: 0.5039 0.5302
>> O2: -0.4753 -0.4928
>> N3: -0.4871 -0.3079
>> H3: 0.4128 0.3422
>> C4: 0.6466 0.5653
>> N4: -0.8363 -0.8737
>> H41: 0.4518 0.4707
>> H42: 0.4518 0.4707
>> C5: -0.4218 -0.3638
>> C6: 0.0028 -0.0362
>>
>> Can you please clarify this point.
>>
>> Regards
>> Asmita
>>
>> On Thu, Jun 28, 2012 at 12:27 PM, FyD <fyd.q4md-forcefieldtools.org>
>> wrote:
>>
>> Dear Asmita,
>>>
>>> > There is a file called all_prot_nucleic10.lib which is provided in
>>> > /amber12/dat/leap/lib folder. The file actually has partial charge
>>> values
>>> > for protonated nucleic acid bases. My doubt is whether this library
>>> could
>>> > be used with recent ff12SB force field for a structure which has both
>>> > standard and protonated nucleic acid bases. And if we can use it, why
>>> do
>>> we
>>> > need to do a separate Gaussian geometry optimization followed by MEP
>>> > calculation for protonated bases.
>>>
>>> if this FF library file contains what you need Yes you can use/test it
>>> with the FF of your choice.
>>>
>>> in general one derives charges and build FF library(ies) only for new
>>> molecule(s)/fragment(s).
>>>
>>> regards, Francois
>>>
>>
>
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Jul 04 2012 - 09:30:03 PDT
