Re: AMBER: Sample more conformational space

From: Carlos Simmerling <>
Date: Wed, 02 Mar 2005 11:35:18 -0500

one possibility is that your simulation is pretty short.
another is the restraints- it isn't clear to me what you are
restraining and what you are not. is the peptide unrestrained?
is the peptide tightly packed in the protein?
you might want to start out by trying to increase sampling
of just the peptide by itself in solution, and when you have
decided on something that works well, try it out for the

this is a hard problem that will not be solved by a short MD simulation...

Bogos Agianian wrote:

>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
>#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
>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
> &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'
>..but the peptide is not moving a lot. Is there a good way to give it a
>Thanks in advance
>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.
>The AMBER Mail Reflector
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Received on Wed Mar 02 2005 - 16:53:02 PST
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