Quoting Mingfeng Yang <mfyang.gmail.com>:
> I am trying to fit the charges for a trifluoroethanol molecule
TFE is in R.E.DD.B. See projects W-15 and W-16
For examples of organic solvents see W-46
http://www.u-picardie.fr/labo/lbpd/REDDB/up/W-46/
For examples of many different alcohols see the work of C. Cezard;
project W-79
http://www.u-picardie.fr/labo/lbpd/REDDB/up/W-79/
> with the
> help of RED. GAMESS(6-31G*) was used to optimize the structure and
> calculate the molecular electrostatic potential, and RESP was used to
> fit the charges in two steps.
>
> My problem is that the charge output from the first and the second step
> are exactly the same. The chemically equivalent atoms were not set to
> have the same charges. What should I do to get the same charges for the
> fluorine atoms binding to the same carbon atom?
See for example the RESP inputs used for project W-16 (2 conformations
and 4 orientations)
http://www.u-picardie.fr/labo/lbpd/REDDB/up/W-16/input1.in
http://www.u-picardie.fr/labo/lbpd/REDDB/up/W-16/input2.in
> The input for stage1 RESP automatically generated by RED is:
> Molecule
> &cntrl
> ioutopt=1, iqopt=1, nmol=1, ihfree=1, irstrnt=1, qwt= 0.0005
> &end
> 1.0
> Molecule
> 0 9
> 6 0
> 9 0
> 9 0 -> 2 !!!
> 9 0 -> 2 !!!
> 6 0
> 1 0
> 1 0
> 8 0
> 1 0
>
> The one for stage 2 RESP is:
> Molecule
> &cntrl
> ioutopt=1, iqopt=2, nmol=1, ihfree=1, irstrnt=1, qwt= 0.001
> &end
> 1.0
> Molecule
> 0 9
> 6 -1
> 9 -1
> 9 -1
> 9 -1
> 6 -1 => 0 !!!
> 1 -1 => 0 !!!
> 1 -1 => 6 !!!
> 8 -1
> 1 -1
Concerning charge equivalencing of chemically equivalent atoms
implementation in R.E.D. please read the tutorial and do the Ethanol
tutorial.
TFE atom names you could use in the pdb R.E.D. input could be:
C1 F2 F2 F2 CT3 H3 H3 O4 H4
This will change in R.E.D. III with a new script Ante_R.E.D.III...
regards, Francois
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Oct 29 2006 - 06:07:37 PST
