From: Jovan Dragelj (jovandragelj_at_gmail.com)
Date: Fri Nov 29 2019 - 02:46:04 CST
Thanks for your answer.
QM/MM is one way to describe this system considering the lack of parameters
but the goal here is to run MD simulations of over 500ns followed by GaMD.
My question was more in the direction of which of those methods I presented
can be used to achieve reasonable rigidity of one part of the protein.
On Thu, Nov 28, 2019 at 10:54 PM Victor Kwan <vkwan8_at_uwo.ca> wrote:
> Have you considered QM/MM?
> Don't think NAMD have support for rigid bodies.
> On Thu, Nov 28, 2019 at 4:17 PM Jovan Dragelj <jovandragelj_at_gmail.com>
>> I have problems finding a proper way to simulate rigid body with NAMD.
>> The system is an enzyme with a metal cluster for which we do not have FF
>> parameters and want it treated as a rigid body. Protein needs to be able to
>> rotate fully, therefore *fixing *atoms won't help.
>> Unfortunately, I could not make any simulation stable (let's assume other
>> simulation conditions are fine, since we using relatively standard
>> 1. I tried using *freeEnergy *feature with urestraint, by defining ref
>> values from the crystal structure and high(er) constants, bond 500, angles
>> 100, barrier for dihedrals 1.0
>> 2. If using *extraBonds *feature, how is this approach any different
>> than number 1.? I tried this with same values as in 1.
>> 3. I have not tested this but, can this be achieved by using simply high
>> *constraints* on atoms? Note: We do not have any FF parameters apart
>> from partial charges.
>> Details: CHARMM36 FF, NAMD 2.13
>> Any help would be highly appreciated.
-- Dr. Jovan Dragelj AG Mroginski Biomolecular Modeling Institute of Chemistry Technical University Berlin Strasse 17. Juni 135 10623 Berlin e-mail: jovan.dragelj_at_tu-berlin.de <jovan.dragelj_at_campus.tu-berlin.de> Mobile: +49-176-27091982 Tel(office): +49-30-314-26516
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