Hello,
I've also copied this to the mailing list, which is where all replies
to such threads should be sent. You can use ntr=1 and set a restraint
weight and a restraint mask that selects all protein residues. This
should have the effect you're looking for. These features are
well-documented in the manual.
Good luck!
Jason
On Fri, Mar 12, 2010 at 10:42 AM, rui <ruisher.gmail.com> wrote:
> Hi, Jason,
>
> Thanks for your reply. When I try to minimize the structure, is there anyway
> that I can keep the protein frozen and only minimize the ligand and the
> covalent bonded residues? Looks like my structure change a lot (RMSD 2A),
> and I'm wondering if I can fix some part of it. Thanks.
>
> On Tue, Mar 9, 2010 at 2:01 PM, Jason Swails <jason.swails.gmail.com> wrote:
>>
>> Hello,
>>
>> On Tue, Mar 9, 2010 at 1:37 PM, rui <ruisher.gmail.com> wrote:
>> > Hi, All,
>> >
>> > I need to calculate/minimize the energy for a protein ligand complex,
>> > the
>> > protein and the ligand is covalently bonded, is amber able to handle
>> > this
>> > problem? If so, can anyone suggest how to do it? Thanks.
>>
>> A covalently bound "ligand" is treated no differently than any other
>> amino acid residue in a protein. The manual and tutorial page (
>> www.ambermd.org/tutorials ) give a good introduction on using Amber.
>>
>> Good luck!
>> Jason
>>
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> ---------------------------------------
>> 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
>
>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Mar 12 2010 - 09:30:04 PST
