Dear Saurabh
The NaN’s essentially mean that certain energies are infinity.
This normally occurs because you have a bad starting structure, often due to
two atoms sitting on top of each other. Unfortunately seeing step 900 doesn’t
help much. It would be much easier to see the very first step and see if any
energies there are reported as NAN, or *’s or just very large. If you can post
this it might be easier to see what is wrong. Part of the output on the step
line lists the atom with the largest force. If there are problems with the
structure this gives you an idea of the first place to look.
The two Selenium atoms are very concerning – where did you get
the parameters for these? What did you do with them? Often selenium atoms are
used by crystallographers as part of the structure solving and thus are not
part of the structure in a biologically relevant context. I’m not sure though
if they are additional or used to replace something else in the protein like
zinc or iron. If they are just additional then you should probably just delete
them. If they substituted something else then you will need to modify the pdb
to change them to the correct atoms in the biological context. You’d then need
to add the missing parameters for these atoms.
In the meantime please post the energies from step zero / one
and also post more details about the structure and how you set it up, input
file etc.
All the best
Ross
From:
owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of saurabh
agrawal
Sent: Saturday, April 26, 2008 4:36 AM
To: amber users
Subject: AMBER: .... RESTARTED DUE TO LINMIN FAILURE ...
|
Dear Amber Users,
I am trying to simulate nucleotide ligand complex. But It aborted during the
simulation once I reduce the restraints below 20 in the input file and gives
the following error.
NSTEP
ENERGY
RMS
GMAX NAME
NUMBER
900
NaN
NaN
0.0000E+00 H5T
1
BOND = NaN
ANGLE =
NaN
DIHED = NaN
VDWAALS = -140.5901
EEL =
NaN
HBOND
= 0.0000
1-4 VDW =
NaN 1-4 EEL
= NaN
RESTRAINT = NaN
EAMBER = NaN
NSTEP
ENERGY
RMS
GMAX NAME
NUMBER
1000
NaN
NaN
0.0000E+00 H5T
1
BOND =
NaN
ANGLE =
NaN
DIHED = NaN
VDWAALS = -140.5901
EEL =
NaN
HBOND
= 0.0000
1-4 VDW =
NaN 1-4 EEL
= NaN
RESTRAINT = NaN
EAMBER = NaN
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
.... RESTARTED DUE TO LINMIN FAILURE ...
The same nucleotide I have simulated with different ligands and those
run fine. This ligand is having two Selenium atoms (which is not
defined in the leap). Is this the reason for the problem?
Every time it is stopping, and I am unable to solve it.
Please help me in this regard.
saurabh
|
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