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
