Dear Gustavo
Here is the list of the used parameter sets as it appears on the out file
of the suspending protein-ligand QM/MM calculation:
Parameter files:
TYP (AT) TYP (AT) SK integral FILE
| 1 1 (C ) 1 (C ) /apps/amber16/dat/slko/C-C.skf
| 2 1 (C ) 2 (H ) /apps/amber16/dat/slko/C-H.skf
| 3 1 (C ) 3 (N ) /apps/amber16/dat/slko/C-N.skf
| 4 1 (C ) 4 (O ) /apps/amber16/dat/slko/C-O.skf
| 5 1 (C ) 5 (S ) /apps/amber16/dat/slko/C-S.skf
| 6 1 (C ) 6 (Br) /apps/amber16/dat/slko/C-Br.skf
| 7 1 (C ) 7 (Zn) /apps/amber16/dat/slko/C-Zn.skf
| 8 2 (H ) 1 (C ) /apps/amber16/dat/slko/H-C.skf
| 9 2 (H ) 2 (H ) /apps/amber16/dat/slko/H-H.skf
| 10 2 (H ) 3 (N ) /apps/amber16/dat/slko/H-N.skf
| 11 2 (H ) 4 (O ) /apps/amber16/dat/slko/H-O.skf
| 12 2 (H ) 5 (S ) /apps/amber16/dat/slko/H-S.skf
| 13 2 (H ) 6 (Br) /apps/amber16/dat/slko/H-Br.skf
| 14 2 (H ) 7 (Zn) /apps/amber16/dat/slko/H-Zn.skf
| 15 3 (N ) 1 (C ) /apps/amber16/dat/slko/N-C.skf
| 16 3 (N ) 2 (H ) /apps/amber16/dat/slko/N-H.skf
| 17 3 (N ) 3 (N ) /apps/amber16/dat/slko/N-N.skf
| 18 3 (N ) 4 (O ) /apps/amber16/dat/slko/N-O.skf
| 19 3 (N ) 5 (S ) /apps/amber16/dat/slko/N-S.skf
| 20 3 (N ) 6 (Br) /apps/amber16/dat/slko/N-Br.skf
| 21 3 (N ) 7 (Zn) /apps/amber16/dat/slko/N-Zn.skf
| 22 4 (O ) 1 (C ) /apps/amber16/dat/slko/O-C.skf
| 23 4 (O ) 2 (H ) /apps/amber16/dat/slko/O-H.skf
| 24 4 (O ) 3 (N ) /apps/amber16/dat/slko/O-N.skf
| 25 4 (O ) 4 (O ) /apps/amber16/dat/slko/O-O.skf
| 26 4 (O ) 5 (S ) /apps/amber16/dat/slko/O-S.skf
| 27 4 (O ) 6 (Br) /apps/amber16/dat/slko/O-Br.skf
| 28 4 (O ) 7 (Zn) /apps/amber16/dat/slko/O-Zn.skf
| 29 5 (S ) 1 (C ) /apps/amber16/dat/slko/S-C.skf
| 30 5 (S ) 2 (H ) /apps/amber16/dat/slko/S-H.skf
| 31 5 (S ) 3 (N ) /apps/amber16/dat/slko/S-N.skf
| 32 5 (S ) 4 (O ) /apps/amber16/dat/slko/S-O.skf
| 33 5 (S ) 5 (S ) /apps/amber16/dat/slko/S-S.skf
| 34 5 (S ) 6 (Br) /apps/amber16/dat/slko/S-Br.skf
| 35 5 (S ) 7 (Zn) /apps/amber16/dat/slko/S-Zn.skf
| 36 6 (Br) 1 (C ) /apps/amber16/dat/slko/Br-C.skf
| 37 6 (Br) 2 (H ) /apps/amber16/dat/slko/Br-H.skf
| 38 6 (Br) 3 (N ) /apps/amber16/dat/slko/Br-N.skf
| 39 6 (Br) 4 (O ) /apps/amber16/dat/slko/Br-O.skf
| 40 6 (Br) 5 (S ) /apps/amber16/dat/slko/Br-S.skf
| 41 6 (Br) 6 (Br) /apps/amber16/dat/slko/Br-Br.skf
| 42 6 (Br) 7 (Zn) /apps/amber16/dat/slko/Br-Zn.skf
| 43 7 (Zn) 1 (C ) /apps/amber16/dat/slko/Zn-C.skf
| 44 7 (Zn) 2 (H ) /apps/amber16/dat/slko/Zn-H.skf
| 45 7 (Zn) 3 (N ) /apps/amber16/dat/slko/Zn-N.skf
| 46 7 (Zn) 4 (O ) /apps/amber16/dat/slko/Zn-O.skf
| 47 7 (Zn) 5 (S ) /apps/amber16/dat/slko/Zn-S.skf
| 48 7 (Zn) 6 (Br) /apps/amber16/dat/slko/Zn-Br.skf
| 49 7 (Zn) 7 (Zn) /apps/amber16/dat/slko/Zn-Zn.skf
Hope this helps.
Thanks.
Amani
On Sat, 19 Aug 2017 at 02:51, Gustavo Seabra <gustavo.seabra.gmail.com>
wrote:
> Dear Amani,
>
> > Em 18 de ago de 2017, à(s) 19:37, Amani Eshtiwi <eshtiwia2017.gmail.com>
> escreveu:
> >
> > On Fri, 18 Aug 2017 at 21:02, Gustavo Seabra <gustavo.seabra.gmail.com>
> > wrote:
> >
> >> Dear Armani,
> >>
> >> What version of sander are you using? Is it the last version?
> >>
> >> There was a problem with the use of halogens parameter sets, which I
> >> believe was solved in the most recent update. Please take a look at the
> >> discussion here:
> >>
> >> http://archive.ambermd.org/201602/0069.html
> >>
> >> HTH,
> >> —
> >> Gustavo Seabra
> >
> >
> > Dear Gustavo
> >
> >
> > Thank you very much for your reply.
> > I am using Amber 16 Sander 2016. Which version shall I use?
>
> The problem should be corrected in this version. But just to be on the
> safe side, I’d recommend you use the most up-to-date one anyways.
>
> What parameter set are you using? Can you tell us the name of the set?
>
> Gustavo.
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Received on Fri Aug 18 2017 - 19:30:02 PDT
