AMBER Archive (2005)

Subject: AMBER: Minimization in sander and nmode

From: Mingfeng Yang (mfyang_at_gmail.com)
Date: Thu Sep 29 2005 - 18:01:24 CDT

I am trying to do a normal mode analysis on a protein with 1363 atoms.
(Amber7 is being used)

At first, I managed to minimize the structure with sander to
DRMS=9.5777E-05. Then, I tried to do NMA on the minimized strucutre with
nmode, however, nmode complain the rms of step length (1.5) is larger
than the drms value (0.0001). So Newton-Raphson method in nmode was used
to further minimized the structure. Now, more than 12 hours past, the
rms of step length is still wandering between 0.01 and 0.05. It seems it
will take forever to reach the drms threshold.

Here is my input file for sander minimization:
/
&cntrl
maxcyc=100000, ntmin=1, ncyc=10, dx0=0.00001, drms=0.0001, imin=1,
cut=99.0, ntb=0, ntp=0, ntp
r=100, ntwr=500,
&end/

Input file for nmode minimization:
/&cntrl
&data
ntrun=4,
maxcyc=10000
drms=0.0001
cut=999,
dielc=1.0,
nvect=100,
idiel=0,
ntx=1,
scee=1.2,
&end/

Did I do anything wrong here? Or, this is a normal situation.

Thanks a lot for any hints!

Happy simulating!
Yang

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