Dear Mijiddorj,
As you can read in the Amber manual in section "3.2.1. Proteins", FF14SB
evolved, ultimately, from FF99. VdW parameters should thus be the same, so
if DOCK6 only uses vdw terms, choose vdw_AMBER_parm99.
Note that this is really a question about DOCK6, so further questions are
better directed to an appropriate mailing list or forum!
Best,
Marc
On 29 April 2016 at 06:03, Mijiddorj Batsaikhan <b.mijiddorj.gmail.com>
wrote:
> Hi Dwight,
>
> Thank you,
> I mean Calculation paramters of Dock6 are vdw_AMBER_parm94, 96, 99.
> I would like to use AMBER FF14SB force field to molecular docking using
> DOCK6. How can I use the force field?
>
> Best regards,
>
> Mijiddorj
>
> On Thu, Apr 28, 2016 at 10:53 PM, Dwight McGee <dwight.mcgee.gmail.com>
> wrote:
>
> > Hi Mijiddorj,
> >
> > You can employ ambpdb to create a mol2 file of your receptor from your
> > topology and coordinate files that has SYBYL atom types, which is
> required
> > by DOCK6.
> >
> > This feature will be available in upcoming release of AMBER 16 but it
> > should be available in the github version of cpptraj if you need it
> > immediately.
> >
> > Best,
> > Dwight
> >
> > On Thu, Apr 28, 2016 at 6:20 AM, Mijiddorj Batsaikhan <
> > b.mijiddorj.gmail.com
> > > wrote:
> >
> > > Dear users,
> > >
> > > I would like to use FF14SB force field to molecular docking using
> DOCK6.
> > > How can I use the force field? Do you have any suggestions?
> > >
> > > Mijiddorj
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > T. Dwight McGee Jr.
> >
> > dwight.mcgee.gmail.com
> >
> > "Problems cannot be solved at the same level of awareness that created
> > them."
> > Albert Einstein
> > _______________________________________________
> > 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
>
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Received on Fri Apr 29 2016 - 01:30:07 PDT
