Dear William,
> Dear AMBERI have a doubt about my RESP charge generation and hope
> someone could help me.I want to calculate the RESP charge of a
> phenol with EP on oxygen atom. I have used the following resp.in
> Phenol-EP &cntrl nmol=1, ihfree=1, iqopt=1, &end
> 1.0 PhenolEP 0 13 6 0 1 0 6 0 1 0 6
> 0 1 0 6 3 1 4 6 1 1 2 6 0 8 0
> 1 0 0 0
Your RESP "input 1" looks difficult to understand ;-)
> Here, I did only one step because there is no methyl groups, used
> the default qwt value (0.0005) and made constrains on similar atoms
> to be charge equally.Is that right?Sorry for any inconvenience but I
> always use RED program, but it does not support EP.
If you look in R.E.DD.B. for a small molecule; a similar one: Toluene
Use the "Download projects" tool of R.E.DD.B.
-- R.E.DD.B. code (if known)
-- Molecule keyword
-- Molecule name Toggle on
-- Author lastname
-- Theory level/Basis set
Text Toluene
You get among others:
Search... [Done]
Result(s) for search by Molecule name Benzene
Project name Benzene
Project code W-41
i.e.
http://q4md-forcefieldtools.org/REDDB/projects/W-41/
If you want to look at the corresponding resp "input 1":
http://q4md-forcefieldtools.org/REDDB/projects/W-41/input1.in
& the resp "input 2":
http://q4md-forcefieldtools.org/REDDB/projects/W-41/input2.in
Let's make the resp "input 1" more simple using a single molecular
orientation:
RESP-A1 project. RESP input generated by R.E.D.
&cntrl
ioutopt=1, iqopt=1, nmol=1, ihfree=1, irstrnt=1, qwt= 0.0005
&end
1.0
Toluene
0 15 Column not used by RESP (Added by R.E.D. for information)
6 0 1
1 0 2
1 0 3
1 0 4
6 0 5
6 0 6
1 0 7
6 0 8
1 0 9
6 0 10
1 0 11
6 8 12: means "12" is made equivalent to "8"
1 9 13
6 6 14
1 7 15
Here, you want to remove the methyl group and add an O & H (by now, 13
atoms in total instead of 15).
For phenol without EP R.E.D. generates the following 1st RESP input:
RESP-A1 project. RESP input generated by R.E.D.
&cntrl
ioutopt=1, iqopt=1, nmol=1, ihfree=1, irstrnt=1, qwt= 0.0005
&end
1.0
Phenol-without-EP
0 13 Column not used by RESP (Added by R.E.D. for information)
8 0 1
1 0 2
6 0 3
6 0 4
1 0 5
6 0 6
1 0 7
6 0 8
1 0 9
6 6 10
1 7 11
6 4 11
1 5 13
For phenol with EP you would need to modify the previous 1st RESP
input a little (here let's suppose the 2 EPs are located at the end of
the PDB or mol2 file in the atom order):
RESP-A1 project. RESP input generated by R.E.D.
&cntrl
ioutopt=1, iqopt=1, nmol=1, ihfree=1, irstrnt=1, qwt= 0.0005
&end
1.0
Phenol-with-EP
0 15 Column not used by RESP (Added by R.E.D. for information)
8 0 1
1 0 2
6 0 3
6 0 4
1 0 5
6 0 6
1 0 7
6 0 8
1 0 9
6 6 10
1 7 11
6 4 11
1 5 13
0 0 14
0 14 15: means "15" is made equivalent to "14"
The second RESP would be:
RESP-A1 project. RESP input generated by R.E.D.
&cntrl
ioutopt=1, iqopt=2, nmol=1, ihfree=1, irstrnt=1, qwt= 0.001
&end
1.0
Phenol-with-EP
0 15 Column not used by RESP (Added by R.E.D. for information)
8 -1 1 -1 is frozen
1 -1 2
6 -1 3
6 -1 4
1 -1 5
6 -1 6
1 -1 7
6 -1 8
1 -1 9
6 -1 10
1 -1 11
6 -1 11
1 -1 13
0 -1 14
0 -1 15
=> all "-1" means all the charges are frozen in the second RESP stage;
(i.e. the charges of the 1st stage are conserved and are not refitted).
Using R.E.D. or any program as a black box is not good (just my
personal opinion). If you want to work on lone pairs, you need to
understand what you do & in particular the format of RESP inputs;
please see:
http://q4md-forcefieldtools.org/RED/resp/
You also need to understand the rules used in the P2N input file in
atomic charge equivalencing; please see:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3
&
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#ATOM-NAME
With Ante_R.E.D. 2.0/R.E.D.-IV many new features are developed but
these rules will remain used.
Finally, if you want to derive charges for a molecule with EP; I would
first run the job _without EP_ and only after _with_ EP; => you will
be able to compare the RESP inputs; the charge values...
This is a quite challenging project... but quite exciting as well ;-)
I hope this helps,
regards, Francois
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Received on Mon May 24 2010 - 00:30:03 PDT
