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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Received on Thu Jul 11 2019 - 06:00:02 PDT
