The initial position of a ligand predicted by AutoDock can be strained
so, in some case, it is necessary to relax it with restraints prior to
long MD run. Also, note that "I am sure about ligand because I used
spdb viewer and computed H-bond. ligand was correct place." is really
not a strong argument.
On Wed, Jul 13, 2011 at 1:05 PM, e p <epepgene1.gmail.com> wrote:
> restraints in active site? in residues that interaction with ligand?
> Do not the vibrations limit?
> are you sure?
> Thanks a lot
>
> On Tue, Jul 12, 2011 at 11:45 PM, Dmitry Nilov <nilovdm.gmail.com> wrote:
>
>> Just run preliminary equilibration stage with restraint prior to MD
>> without restraints.
>>
>> On Wed, Jul 13, 2011 at 9:35 AM, e p <epepgene1.gmail.com> wrote:
>> > Dear Dmitry
>> > I dont want to limit the vibrations because I want to study about
>> vibrations
>> > in active site .
>> > Do you know that the restraints in active site limit the vibration or
>> not?
>> > thanks for your answer
>> > Best
>> >
>> >
>> > On Tue, Jul 12, 2011 at 4:30 AM, Dmitry Nilov <nilovdm.gmail.com> wrote:
>> >
>> >> I would restrain the distance between ligand atoms involved in
>> >> catalysis and active site residues at the equilibration stage. What is
>> >> the reason to apply restraint on atoms that are not involved in
>> >> catalysis?
>> >>
>> >> > I want to inspect the effect of connection of a ligand to my protein
>> >> before
>> >> > formation of a covalent bond to the active site. I have designed a
>> new
>> >> > ligand and put it to the active site by auto dock. the ligand moved
>> >> during
>> >> > MD run so I had to put dist restraints(rk2=50,) on ligand atoms that
>> are
>> >> not
>> >> > involved in catalysis and on 5 residues of the protein out of the
>> active
>> >> > site. it didnt solve the problem. the ligand still moves and
>> rotates.As I
>> >> > want to study the vibrations before formation of nucleophilic attack,
>> I
>> >> dont
>> >> > want to use restraints to limit active site vibrations.
>> >> > Any offer would be apprecited.
>> >> >
>> >> >
>> >> > Elahe
>> >> > _______________________________________________
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>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >> Dmitry Nilov
>> >> Faculty of Bioengineering and Bioinformatics,
>> >> Lomonosov Moscow State University
>> >> web: http://enzyme.fbb.msu.ru/
>> >>
>> >> _______________________________________________
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>> >>
>> > _______________________________________________
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>> > AMBER.ambermd.org
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>> >
>>
>>
>>
>> --
>> Dmitry Nilov
>> Faculty of Bioengineering and Bioinformatics,
>> Lomonosov Moscow State University
>> web: http://enzyme.fbb.msu.ru/
>>
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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>
--
Dmitry Nilov
Faculty of Bioengineering and Bioinformatics,
Lomonosov Moscow State University
web: http://enzyme.fbb.msu.ru/
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Received on Wed Jul 13 2011 - 03:00:03 PDT
