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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Received on Thu Oct 29 2009 - 06:00:02 PDT
