hi,
thank you for your answers.
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.
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).
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. 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.
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?
Greetings
Thomas
On 12/10/2010 09:08 AM, FyD wrote:
> Thomas,
>
> I would run R.E.D. III.4 or R.E.D. Server to see how "multiple
> molecule orientations" versus "single molecule orientation" works.
> "Multiple molecule orientations" was first defined/introduced in
> R.E.D.-I more than 7 years ago.
>
> If you are interested in "multiple molecule orientations", we have
> differentiated translation, rotation& reorientation
> (translations+rotations) in III.4& IV June 2010.
> See http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#QMRAALGO
> http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#RBRAALGO
>
> ---
>
> Now to answer to your problem if you do want to do all "manually", you
> need to remove the \n characters between two concatenated espot files.
> Unfortunately, this is not documented in the RESP documentation:
> http://q4md-forcefieldtools.org/RED/resp/
> We should update it once again...
>
> I just ran a job using the R.E.D. Server public account for
> Ethane-1,2-diol with two molecular orientations; the corresponding
> data are in R.E.DD.B.
> http://q4md-forcefieldtools.org/REDDB/projects/W-26/
> The R.E.D. Server job is at the following web address:
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFkxhAzDk4ADFDUADFSRoSe8VbADFm7bny0Mq81/P448.html
>
> the two espot files are .
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFkxhAzDk4ADFDUADFSRoSe8VbADFm7bny0Mq81/P448/Data-R.E.D.Server/espot_m1-1-1
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFkxhAzDk4ADFDUADFSRoSe8VbADFm7bny0Mq81/P448/Data-R.E.D.Server/espot_m1-1-1
> versus the concatenated one:
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFkxhAzDk4ADFDUADFSRoSe8VbADFm7bny0Mq81/P448/Data-R.E.D.Server/espot_m1
> in the middle of this file, you need to have:
>
> [...]
> 1.6328600E-02 6.2478800E+00 7.9238200E+00 -2.8277400E+00
> 7.8977100E-03 7.7364200E+00 6.1182200E+00 -4.0862000E+00
> 8.7084000E-03 5.7686100E+00 6.1182200E+00 -4.0862000E+00
> 10 565 0 Ethane-1,2-diol
> 3.6445546E+00 2.5319613E+00 0.0000000E+00
> 5.4308516E+00 2.6101138E+00 -1.4173000E-06
> 2.8593587E+00 0.0000000E+00 0.0000000E+00
> [...]
>
>
> and not something like
> [...]
> 1.6328600E-02 6.2478800E+00 7.9238200E+00 -2.8277400E+00
> 7.8977100E-03 7.7364200E+00 6.1182200E+00 -4.0862000E+00
> 8.7084000E-03 5.7686100E+00 6.1182200E+00 -4.0862000E+00
>
>
>
> 10 565 0 Ethane-1,2-diol
> 3.6445546E+00 2.5319613E+00 0.0000000E+00
> 5.4308516E+00 2.6101138E+00 -1.4173000E-06
> 2.8593587E+00 0.0000000E+00 0.0000000E+00
> [...]
>
>
> Finally, you need to be sure that your two RESP inputs are correct&
> you did not forget the add the section related to inter-orientation
> charge equivalencing.
> This is documented in the RESP documentation:
> http://q4md-forcefieldtools.org/RED/resp/
>
> See in R.E.DD.B.
> http://q4md-forcefieldtools.org/REDDB/projects/W-23/input1.in
> http://q4md-forcefieldtools.org/REDDB/projects/W-23/input2.in
> & in the R.E.D. Server job:
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFkxhAzDk4ADFDUADFSRoSe8VbADFm7bny0Mq81/P448/Data-R.E.D.Server/input1_m1
> http://cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFkxhAzDk4ADFDUADFSRoSe8VbADFm7bny0Mq81/P448/Data-R.E.D.Server/input2_m1
>
> I hope this helps.
>
> regards, Francois
>
>
>> Dear all,
>> i have a problem with the resp charge generation with multiple molecule
>> orientations.
>> I used the following protocol:
>> * Run gaussian with 4 different orientations
>> * extract esp data
>> espgen -i gau.out -o *.esp
>> * put the *.esp files together
>> cat *.esp> all.esp
>> * then generating *.ac file etc
>> antechamber -fi gout -i gau.out -fo ac -o wo_resp.ac
>> * doing resp fit
>> respgen -i wo_resp.ac -o m.respin1 -f resp1 -n 4
>> respgen -i wo_resp.ac -o m.respin2 -f resp2 -n 4
>> resp -O -i m.respin1 -o m.respout1 -e all_esp.esp -t qout1
>> resp -O -i m.respin2 -o m.respout2 -e all_esp.esp -q qout1 -t qout2
>> * reading charge
>> antechamber -i wo_resp.ac -fi ac -o w_resp.ac -fo ac -c rc -cf qout2
>> * looking for missing parameters
>> parmchk -i w_resp.ac -f ac -o frcmod
>> * puting all together
>> antechamber -i w_resp.ac -fi ac -o w_resp.mol2 -fo mol2 -at gaff -rn MOL
>> * running teLeap
>> teLeap -f leap.in
>>
>> If i do the above stuff for each orientation individually, i get 4
>> different sets of charge.
>> If i do the above stuff, i get the set of charges corresponding to the
>> orientation which is first mentioned in the all.esp. So it seems to me
>> that from the 4 sets of esp-data, only the frist one is read/used.
>>
>> Has anybody an idea where my mistake lies?
>>
>> Greetings
>> Thomas
>
>
>
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Received on Fri Dec 10 2010 - 04:30:03 PST
