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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>
--
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 - 00:00:02 PDT
