AMBER Archive (2009)

Subject: [AMBER] implicit solvent simulation

From: Manish Kumar (kumarmanish.amb_at_gmail.com)
Date: Wed Aug 05 2009 - 23:49:30 CDT

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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