Dear�Professor�David
Thanks for answering my email.
I missed writing 10^5 for energy values.
The energies of the calculated steps using�LBFGS method:
NSTEP � �1 � � � � � �ENERGY � � � �-5.7810E+05
NSTEP � � 27 � � � �ENERGY � � � ��-5.2950E+05
The NSTEP is the final result.
The input of my job is:
�&cntrl
�imin � = 1,
�maxcyc = 100000,
�drms � = 1.0E-5,
�ntb � �= 0,
�ntmin = 3,
�cut � �= 15.0,
�ntb=0,
�igb=0,
/
�&lmod
�xmin_method = "LBFGS"
/
Is that normal?
as well, using TNCG method, gives unrealistic optimized structure of the complex, where the ligand pushed out the active site.�
In addition, the final energy of the TNCG is higher than LBFGS. I read that TNCG is better than LBFGS, isn't it?
Cheers;
----- Original Message -----
From: David A Case <case.biomaps.rutgers.edu>
To: Anglea A. <a.anglea90.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Cc:
Sent: Wednesday, November 2, 2011 11:47 AM
Subject: Re: [AMBER] Minimization in sander
On Wed, Nov 02, 2011, Anglea A. wrote:
> I used LBFGS method for sander minimization. The initial energy of the
> complex is -5.78 and the final energy is -5.29 kcal.mol-1. why the final
> energy is higher than the initial energy?
We'd have to see the details.� Minimizations are not guaranteed to be
monotonically decreasing.� What caused the minimization to stop?� Was it
because it had reached the requested maximum number of cycles?� Also, having a
protein/ligand total energy be so close to zero is rather unusual.� I think
we would have to see your inputs and outputs to be of much help.
...dac
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Received on Wed Nov 02 2011 - 05:30:05 PDT
