AMBER Archive (2009)

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

From: moitrayee_at_mbu.iisc.ernet.in
Date: Thu Oct 29 2009 - 07:36:13 CDT

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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