AMBER Archive (2009)

Subject: [AMBER] implicit solvent simulation

From: Manish Kumar (
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:

  ntr=1, restraintmask=':1-215',

Heating Script is:

  ntpr=1000, ntwx=0,
  ntt=3, gamma_ln=2.0,
  tempi=0.0, temp0=300.0,
  ntr=1, restraintmask=':1-215',
 &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.

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