Dear Amber Users,
I built my starting structure and ran a simulation to obtain an equilibrated
system along the same lines shown in the MM PBSA tutorial section 1. When I
was visualizing the mdcrd files using VMD I saw that the atoms are totally
hapazard and randomly connected.
minimise hn
&cntrl
imin=1,maxcyc=1000,ncyc=500,
cut=10.0,ntb=1,
ntc=2,ntf=2,
ntpr=100,
ntr=1, restraintmask=':1-23',
restraint_wt=2.0
/
heat hn
&cntrl
imin=0,irest=0,ntx=1,
nstlim=50000,dt=0.002,
ntc=2,ntf=2,
cut=10.0, ntb=1,
ntpr=500, ntwx=500,
ntt=3, gamma_ln=1.0,
tempi=0.0, temp0=300.0,
ntr=1, restraintmask=':1-23',
restraint_wt=2.0,
nmropt=1
/
&wt TYPE='TEMP0', istep1=0, istep2=25000,
value1=0.1, value2=300.0, /
&wt TYPE='END' /
Can someone suggest me, which place I am possibly going wrong? I can provide
more information if necessary. Do I need to give stronger restraints?
Thanks,
Jagdeesh
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Received on Fri Jan 22 2010 - 18:30:02 PST
