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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>
--
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 - 07:30:02 PDT
