AMBER Archive (2007)

Subject: AMBER: PMF calculation

From: Jena M (jeninhas_at_hotmail.com)
Date: Mon Jun 25 2007 - 14:59:02 CDT

Hi
 
 
I am having some difficulties in creating the umbrella sampling input file. I want to calculate PMF of a ligand moving from 8 Å to 2 Å of a residue, keeping the protein residues within 5 angstroms of the ligand and of the residue frozen. I want to decrease the distance at 0.2 Å intervals. So, for instance for the first window do I have to set r2=r3=7.8? Here is my complete input file:
 
&cntrl
  imin = 1,
  ntmin = 0,
  maxcyc = 3000,
  ntb = 1,
  nmropt=1,
  ntr = 1,
  restraint_wt=200.0,
  restraintmask='!:566,667 <:5 | (!:566,667)',
  cut = 10
 /
 &wt type='DUMPFREQ', istep1=10 /
 &wt type='END' /
DISANG=dist.restraint
DUMPAVE=dist.result
 
#distance restrainst
&rst iat=662,667, r1=0.0, r2=7.8, r3=7.8, r4=100.0, rk2 =100., rk3 = 100.,
 iresid=1,
 ATNAM(1)='SG',
 ATNAM(2)='C2',
/
 
As far as I understood we have two ways to prepare the input files for each window/simulation. One is to use the configuration of the previous window as input for the next window. The second one is to use always the same input file for each window. Is this correct? Which of the methods is better?
 
Any help is highly appreciated
Thanks
Jena
 
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