On Thu, Apr 15, 2010 at 11:01 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> Does minimization use PME?
If not, then my suggestion certainly won't work :). I thought it did
though, and that of course is based on no code-searching, but also a
scan of the manual turned up no warnings that it did not work...
Perhaps someone that knows for sure can chime in.
All the best,
Jason
>
> Bill
>
>> Take a look at the imin=3D5 option in sander (manual). That will let
>> you process a trajectory just as though it were a series of input
>> coordinate files. Choosing a maxcyc of 0 or 1 will simply extract the
>> energies. I believe you are able to set ntb=3D1 or 2 (equivalent in the
>> case of a single-point energy calculation I believe). You can then
>> proceed to use ptraj to strip the ligand from the receptor and analyze
>> the receptor alone with this method and the same for the ligand
>> (you'll need separate, compatible prmtops for each step). Then taking
>> the difference complex - receptor - ligand will give you the binding
>> energy. This is basically MM/PBSA with periodic boundary
>> conditions...
>>
>> Good luck!
>> Jason
>>
>> On Thu, Apr 15, 2010 at 1:11 AM, juan zeng <azengjuan.gmail.com> wrote:
>> > Dear amber users:
>> > =A0 =A0 =A0 =A0 =A0I want to calculate the binding affinity on protein-li=
>> gand complex
>> > with the linear interaction energy method,in this environment the binding
>> > affinity comprises Van der waals interaction potential and electrocstatic
>> > interaction potential.while others used the non-periodic boundary conditi=
>> on
>> > to calculate the binding affinity before,now I wish that this calculation
>> > can be done in the periodic boundary condition.but the molecules in cell =
>> far
>> > away from the center cell will interaction with the protein-ligand comple=
>> x
>> > in the center cell,so I need to find out a method that can calculate the
>> > interaction energy(especially the electrostatic interaction energy) of th=
>> e
>> > complex with all other molecules in the whole simulation system.Can you g=
>> ive
>> > me some suggestion how to make this calculation be realized.
>> > =A0 =A0 =A0 =A0Hope receive your reply.
>> >
>> > Juanzeng
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --=20
>> ---------------------------------------
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Graduate Student
>> 352-392-4032
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Apr 15 2010 - 10:00:04 PDT
