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
> > >
> > >
> > > _______________________________________________
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> > > 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
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Received on Thu Jul 11 2019 - 09:00:02 PDT
