Dear Experts,
I am doing implicit solvent simulation.
My tleap commands were:
tleap -s -f leaprc.ff99SB
source leaprc.gaff
loadAmberParams LIG.frcmod
loadAmberPrep LIG_amber.prepc
set default PBradii mbondi2
com = loadpdb PROT_lig.pdb
check com
saveamberparm com cplx_wt_impli.prmtop cplx_wt_impli.inpcrd
Minimization script is:
&cntrl
imin=1,maxcyc=2000,ncyc=1000,
cut=999.0,
igb=5,ntb=0,
ntc=2,ntf=2,
ntpr=100,
ntr=1, restraintmask=':1-215',
restraint_wt=50.0
Heating Script is:
&cntrl
imin=0,irest=0,ntx=1,
nstlim=100000,dt=0.001,
ntc=2,ntf=2,
cut=999.0,
igb=5,ntb=0,
ntpr=1000, ntwx=0,
ntt=3, gamma_ln=2.0,
tempi=0.0, temp0=300.0,
ntr=1, restraintmask=':1-215',
restraint_wt=5.0,
nmropt=1
/
&wt TYPE='TEMP0', istep1=0, istep2=100000,
value1=0.1, value2=300.0, /
&wt TYPE='END' /
I will be very thankful if someone can look over these scripts and assure
me that these are correct.
Manish
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Received on Wed Aug 19 2009 - 20:37:28 PDT
