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 - 00:30:03 PST
