Dear Francois,
thank you for your answer.
I will look more into your data and compare it with mine.
The mesitylene is a solvent in my case, so here the chemical equivalence
should be fulfilled.
For the building blocks of my huge molecule i also thought i should give
up the chemical equivalence (so, thank you for your remark). But i
thought: first understand a single molecule and then go to the building
block stuff.
Greetings
Thomas
On 12/10/2010 05:13 PM, FyD wrote:
> Dear Thomas,
>
>> For the gaussian calculations i used the R.E.D Server and i compared my
>> files with your files given below:
>>
>> The espot_m1* files look from the format the same, and in the
>> concatenated one there are no blanc lines.
>
> ok
>
>> The input1_m1 / input2_m1 file also look similar (only the last
>> paragraph differes because i have 4 and here in the example are 2
>> orientations).
>
> ok
>
>> When i use espot_m1 as an input for respgen / resp of AMBER i get the
>> same problem as before (resp charges correspond to the first molecule of
>> the esp-data).
>> So it seems to me that the problem lies somewhere in the protocol i used
>> for the AMBER stuff.
>
> ...
>
>> With the resp charges of the R.E.D. Server (in Mol_m1-o1.mol2) i have
>> the following problem:
>> My molecule is mesitylene.
>
> so this is http://fr.wikipedia.org/wiki/Mésitylène right ?
>
>> The charges of the hydrogen in the
>> methyl-groups are the same (for each group), but all other charges
>> differ by each other. Since the molecule is symmetric the charges of all
>> 3 methyl-groups should be the same.
>
> Yes
>
>> In your Ethane-1,2-diol example this is not the case (the charges are
>> symmetric, how they should be). Am i missing somewhere a flag or
>> otherstuff, so that the R.E.D. Server recorgnises the symmetrie of the
>> molecule and makes the resp-charges also symmetric?
>
> Chemical equivalencing is defined by Ante_R.E.D. 2.0. in R.E.D. Server
> - bugs are always possible since Ante_R.E.D. 2.0 is quite new - We
> have already corrected many problems ;-)
>
> -1 I just built Mesitylene using the new Java applet for R.E.D. Server
> directly from Toluene... See
> http://q4md-forcefieldtools.org/REDS/faq.php#20
>
> -2 then, I ran Ante_R.E.D. 2.0 for Mésitylène; chemical equivalencing
> seems ok to me in the three cases below:
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFUoqNpfOZADFcQbbQYwYuC0ADFtREA4gyWh0/P449.html
> or
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFTU8R61STADFsFhiMADFy9eIGEq4L6CUpyLADF/P451.html (different
> tree)
> or
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADF15ljaj78ADF8YFAQMUheJZzoAXNbN6cw1/P452.html (different tree
> again)
>
> -3 then, I ran R.E.D. IV using Firefly (since I used the public
> account to share data)
> See http://q4md-forcefieldtools.org/REDS/faq.php#21
>
> charge derivation data are .
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFdPIYY5TgADFebZjZ2EGADFQRn73ptdZnF8ADF/P450.html
> mol2 file is .
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFdPIYY5TgADFebZjZ2EGADFQRn73ptdZnF8ADF/P450/javaappletmol2-1.html
> => charge equivalencing is correctly performed.
> & inputs are correct i think
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFdPIYY5TgADFebZjZ2EGADFQRn73ptdZnF8ADF/P450/Data-R.E.D.Server/input1_m1
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFdPIYY5TgADFebZjZ2EGADFQRn73ptdZnF8ADF/P450/Data-R.E.D.Server/input2_m1
>
> please tell me if I missed something...
>
> regards, Francois
>
> PS Then if you want to involve this building block in some
> macrostructure building you will have to break the chemical
> equivalencing defined by Ante_R.E.D. 2.0...
>
>
>
>
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Received on Mon Dec 13 2010 - 02:30:02 PST
