AMBER Archive (2009)

Subject: Re: [AMBER] [Fwd: ligand exiting a protein cavity]

From: Kshatresh Dutta Dubey (kshatresh_at_gmail.com)
Date: Thu Oct 29 2009 - 09:44:28 CDT

I had faced same problem during the simulation of a protein ligand complex,
when i run the simulation, after 1ns simulation the ligand jumped out of
cavity. I am not sure, but this problem occurs due to the image of the
atom/molecules during simulation, which does not effect quality of
simulation. Simulations in this state are quite well. We may proceed it.
  I am also seeking for others reply so that i can confirm myself.

Kshatresh

On Thu, Oct 29, 2009 at 6:06 PM, <moitrayee_at_mbu.iisc.ernet.in> wrote:

> Some more information along with the problem pasted below.
> I should also mention that the ligand is held by a loop that moves outward
> when
> the ligand departs. Actually this loop in my protein has two states, open
> (in
> the native form) and closed (in the ligand bound form). In the ligand bound
> form, after some time the loop moves out to exit the ligand.
> Please suggest me what to do.
> Thanks a lot.
>
> Sincere Regards,
> Moitrayee
>
> ------------------------------- Original Message
> -------------------------------
> Subject: ligand exiting a protein cavity
> From: moitrayee_at_mbu.iisc.ernet.in
> Date: Thu, October 29, 2009 5:57 pm
> To: "AMBER Mailing List" <amber_at_ambermd.org>
>
> --------------------------------------------------------------------------------
>
> Dear Amber Users,
>
> I am facing a weird problem with my protein.
> The protein has a high resolution crystal structure (2.1 ang.) and is used
> for
> my simulation. It is bound with a ligand for which I derived the parameters
> using Gaussian 03 and antechamber module of AMBER. I do minimizations and
> equillibrations before starting the production run. There is no error as
> such.
> However towards the end of the production run at room temp. the ligands
> exits
> the protein cavity.
> My md.in file is as follows:
>
> &cntrl
> imin=0,
> ntx=7, irest=1,
> ntpr=50, ntwr=500, iwrap=1, ntwx=500, ntwe=50,
> ntf=2, ntb=2, igb=0, scnb=2.0, scee=1.2,
> cut=10.0,
> nscm=50,
> nstlim=5000, dt=0.002,
> tempi=300., temp0=300., ntt=1, tautp=0.5, dtemp=0.,
> ntp=1, taup=0.5,
> ntc=2, tol=0.00001,
> &end
> &ewald
> vdwmeth=1,
> &end
>
> What can be the possible problems ?
>
> Thanks a lot in advance.
>
> Sincere Regards,
> Moitrayee
>
>
>
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