Re: [AMBER] Density for a protein ligand complex run

From: Hector A. Baldoni <hbaldoni.unsl.edu.ar>
Date: Wed, 3 Jun 2015 09:58:49 -0300 (ARGSL-ST)

Hello,

Please, describe your protein with leaprc ff14SB. Run again with the
attached protocol. modify the attached bash file to fit your system and
take care to modify nstlim in the npt file to account for 80 ns. Place a
garlic over the cluster (just in case) and then tells us what has
happened.

Greeting.
Hector.


> Hi Dac and Hector,
>
> The system details are:
> Force field : gaff and ff99SB
> System Length : 212 residues (protein) and one Drug
> Overall Protein is Neutral and Drug has -2 Net charge
> Thermostat and barostat used: Langevin thermostat (NTT=3),
> MC Barostat was default i.e 1, ntp=1
>
>
> My question is, is this density being less than 1gg/cc justifiable in
> terms
> of MD run. Is the run okay?
>
> When I visualize in VMD the trajectory for the drug-protein interaction
> does not any show blow off. Moreover the protein I have used is a modeled
> one. The temperature, pressure, volume and Energies are showing stable
> graphs as expected from a normal 80 ns run.
>
> What can a rmsd data tell about the simulation? Is it necessary for the
> rmsd to get stabilized below 3 or 4 Angstrom in case of modeled protein
> runs as well as there is an non-modeled loop region towards the
> protein-tail.
>
> Thanks
> M. Jones
>
>
> On Wed, Jun 3, 2015 at 1:11 AM, David A Case <case.biomaps.rutgers.edu>
> wrote:
>
>> On Tue, Jun 02, 2015, Mrinda Jones wrote:
>> >
>> > And after simulation run for 80 ns, the summary.DENSITY file shows an
>> > average density of 0.98 which is stable but less than 1 gm/cc.
>>
>> I agree that this seems a little low. But without knowing what force
>> field you used, how big the protein is, what its overall charge is, what
>> thermostat and barostat you used, and so on, it's hard to be of much
>> help.
>>
>> Plus, I almost never use TIP3P water; maybe people on the list can
>> report
>> on what sorts of densities they typically see for a protein in a 12 Ang
>> buffer
>> box of TIP3P water.
>>
>> ...dac
>>
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--------------------------------------
 Dr. Hector A. Baldoni
 Area de Quimica General e Inorganica
 Universidad Nacional de San Luis
 Chacabuco 917 (D5700BWS)
 San Luis - Argentina
 hbaldoni at unsl dot edu dot ar
 Tel.:+54-(0)266-4520300 ext. 6157
--------------------------------------
I DO NOT DEFINE TIME, SPACE, PLACE, AND MOTION, AS BEING WELL KNOWN TO ALL.
-- NEWTON (1642-1726), PRINCIPIA.


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Received on Wed Jun 03 2015 - 06:00:05 PDT
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