AMBER Archive (2005)

Subject: AMBER: Sample more conformational space

From: Bogos Agianian (agianian_at_embl.de)
Date: Wed Mar 02 2005 - 06:52:49 CST

Dear Amber users,
  
Starting from a crystal structure of a protein-peptide complex, I try to model
the binding of the same peptide to very similar isoforms of the protein
(created by homology modeling). The starting structure of the peptide is the
one obtained after 3D-superposition of the homology models onto the crystal
structure of the complex.
  
My question is what is a good protocol in Amber 7.0 to sample as much
conformational space of the peptide as posible so that it gets un-stuck of its
conformation in the crystal.
  
I thought of simulated annealing and performed a run using the following
input, after equilibration (I keep parts of the protein far from the peptide
fixed):
  
#simulated annealing protocol, 50 ps
 &cntrl
    nstlim=50000, imin=0,
    ntc=2, ntf=2,
    ntpr=500, ntt=1, ntwx=500, igb=1,
    cut=20.0, ntb=0, vlimit=10,
    ntr=1,
    nscm=1000,
/
Restrains on residues
1.0
RES 1 30
RES 36 50
RES 52 53
RES 56 58
RES 63 64
RES 67 84
RES 94 139
RES 141 143
RES 145
RES 149 165
END
END
&end
#
#
 &wt type='TEMP0', istep1=0,istep2=6000,value1=0.0,
            value2=600., /
 &wt type='TEMP0', istep1=6001,istep2=15000,value1=600.,
            value2=600., /
 &wt type='TEMP0', istep1=15001, istep2=45000, value1=600.0,
            value2=100.0, /
 &wt type='TEMP0', istep1=45001, istep2=50000, value1=0.0,
            value2=0.0, /
#
#
 &wt type='TAUTP', istep1=0,istep2=6000,value1=1.0,
            value2=1.0, /
 &wt type='TAUTP', istep1=6001,istep2=15000,value1=0.4,
            value2=0.4, /
 &wt type='TAUTP', istep1=15001,istep2=40000,value1=4.0,
            value2=4.0, /
 &wt type='TAUTP', istep1=40001,istep2=45000,value1=1.0,
            value2=1.0, /
 &wt type='TAUTP', istep1=45001,istep2=50000,value1=0.1,
            value2=0.05, /
  
 &wt type='END'
&end
  
  
  
..but the peptide is not moving a lot. Is there a good way to give it a
kick?
  
  
Thanks in advance
  
Bogos
  
  
  
PS: The previous problem I had with joining residues was solved by simply
changing the order of the residues in the pdb file. Thanks for the responses.
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