You can use the same antechamber command but write a .ac file instead
antechamber -fi gout -fo ac -i .gout -o bg6.ac -c resp -at gaff -rn bg6
Then you can use respgen to create the resp input file and the run resp.
This will maintain the same index order I mentioned above.
On Thu, Jul 11, 2019 at 11:50 AM Sadaf Rani <sadafrani6.gmail.com> wrote:
> Dear Kellon
> thank you
> it makes sence for mol2 file but not for prepi
> as I did following:-
>
> antechamber -fi gout -fo prepi -i .gout -o bg6.prepi -c resp -at gaff -rn
> bg6
> Here it is different. If you please could have a look at these 2 files.
> If I want to use respgen program for the output of gaussian is it the same
> file(gout) to convert fisrt in to .ac file and then run in to respgen for 2
> stage fitting?
>
> thank you
>
>
> On Thu, Jul 11, 2019 at 3:19 PM Kellon Belfon <kellonbelfon.gmail.com>
> wrote:
>
> > Hi Sadaf,
> >
> > The second column in the resp.out file represents the atomic number of
> the
> > element. The index of the first column in the resp.out file correspond to
> > the first column in your mol2 file. For example, first index is 1 which
> has
> > an atomic number of 15 (resp.out file) and hence it is a P (mol2 file).
> You
> > will replace the charge 1.352900 in the last column of your mol2 file for
> > index 1 with the optimized charge of 1.304538 from your resp fitting.
> > 1 P 3.8390 123.5530 13.4480 p5 1 LIG 1.352900
> > will become:
> > 1 P 3.8390 123.5530 13.4480 p5 1 LIG 1.30453
> >
> > Hope this is clear. Let me know if you have any other questions.
> >
> > Regards,
> >
> > Kellon
> >
> > On Thu, Jul 11, 2019 at 8:37 AM Sadaf Rani <sadafrani6.gmail.com> wrote:
> >
> > > Hi David and AMBER
> > > I am still confused as how to recognise atoms in resp.out and add
> charges
> > > accordingly?
> > > as format of resp.out is:-
> > > Resp charges for organic molecule
> > >
> > >
> > > Point Charges Before & After Optimization
> > >
> > > no. At.no. q(init) q(opt) ivary d(rstr)/dq
> > > 1 15 0.000000 1.304538 0 0.000382
> > > 2 8 0.000000 -0.937716 0 0.000530
> > > 3 8 0.000000 -0.937716 2 0.000530
> > > 4 8 0.000000 -0.937716 2 0.000530
> > > 5 6 0.000000 0.518773 0 0.000946
> > > 6 8 0.000000 -0.705468 0 0.000702
> > > 7 6 0.000000 0.238018 0 0.001937
> > > 8 8 0.000000 -0.710723 0 0.000697
> > > 9 6 0.000000 0.245035 0 0.001889
> > > 10 8 0.000000 -0.734824 0 0.000674
> > > 11 6 0.000000 0.104696 0 0.003454
> > >
> > >
> > > and for mol2:-
> > >
> > > .<TRIPOS>ATOM
> > > 1 P 3.8390 123.5530 13.4480 p5 1 LIG
> > > 1.352900
> > > 2 O1P 3.1070 124.2090 14.5470 o 1 LIG
> > > -0.747167
> > > 3 O2P 5.1500 124.1140 13.0540 o 1 LIG
> > > -0.747167
> > > 4 O3P 3.7560 122.0800 13.4850 o 1 LIG
> > > -0.747167
> > > 5 C1 0.9050 125.5120 9.0780 c3 1 LIG
> > > 0.355900
> > > 6 O1 1.5480 125.2890 7.8690 oh 1 LIG
> > > -0.627800
> > > 7 C2 -0.5830 125.2840 8.9230 c3 1 LIG
> > > 0.090100
> > > 8 O2 -1.0930 126.1730 7.9430 oh 1 LIG
> > > -0.631800
> > > 9 C3 -1.2720 125.5090 10.2640 c3 1 LIG
> > > 0.015100
> > > 10 O3 -2.6840 125.2920 10.1360 oh 1 LIG
> > > -0.665800
> > > 11 C4 -0.6670 124.5400 11.2730 c3 1 LIG
> > > 0.283100
> > >
> > >
> > > Also I am look on this tutorial
> > > http://ambermd.org/tutorials/advanced/tutorial1/section1.htm but from
> > > where
> > > resp.in file is comming in step iv)?
> > > Any one could you please suggest me.
> > >
> > > thank you
> > >
> > > Sadaf
> > >
> > > On Tue, Jul 9, 2019 at 2:28 PM David Case <david.case.rutgers.edu>
> > wrote:
> > >
> > > > On Sun, Jul 07, 2019, Sadaf Rani wrote:
> > > >
> > > > >I calculated charges for my ligand
> > > > >As per para 10 they have asked to edit atomic charges in prepi file
> > from
> > > > >resp.out file. However I have confusion in recognising atom numbers
> in
> > > > resp
> > > > >out and in my prepi file.
> > > >
> > > > It may be easier to ask antechamber to make a mol2 file (rather than
> > > > prepi), and edit the charges there. But you'll still have to be sure
> > > > that the atom ordering in the resp and mol2 files are the same.
> > > >
> > > > ...dac
> > > >
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> > --
> > Kellon A. A. Belfon, Graduate Student
> > Carlos Simmerling Laboratory
> > The Laufer Center for Physical and Quantitative Biology
> > The Department of Chemistry, Stony Brook University
> > Stony Brook, New York 11794
> > Phone: (347) 546-4237 <(347)+546+4237> Email: kellon.belfon.stonybrook.
> > <kellon.belfon.stonybrook.edu>edu
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
Kellon A. A. Belfon, Graduate Student
Carlos Simmerling Laboratory
The Laufer Center for Physical and Quantitative Biology
The Department of Chemistry, Stony Brook University
Stony Brook, New York 11794
Phone: (347) 546-4237 <(347)+546+4237> Email: kellon.belfon.stonybrook.
<kellon.belfon.stonybrook.edu>edu
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Received on Thu Jul 11 2019 - 10:00:02 PDT
