I forgot to mention that the resp.in file is coming from the respgen
program in antechamber. It reads a .ac file as an input, which also have
the index for each atom in your system.
On Thu, Jul 11, 2019 at 10:18 AM 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
>> >
>> _______________________________________________
>> AMBER mailing list
>> 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
>
--
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 - 07:30:03 PDT
