Hi John,
I assume all of the test cases passed in serial and parallel.
If you look closely at your calculation output you will see that the angle
term is infinite and your vdwaals term is very high. This suggests that you
have a very strained initial structure. It is strange for the angle term to
be infinite (or very large), normally it is bond terms that end up very high
or the EEL/VDW terms.
I would suggest visually looking at your starting structure to see if you
can see what is wrong with - I would focus on atom HE1 (4173) which has the
highest force on it.
All the best
Ross
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
john smith
Sent: Tuesday, December 09, 2008 10:21 PM
To: amber
Subject: AMBER: forrtl severe(174) error with minimization and md
Dear all,
I have compile the AMBER10 and AmberTools1.0 on IBM PC with Intel Pentium 4
processor using RedHat EL4 linux, AMBER was compiled with inter fortran
compiler. All the test have passed during the installation.
And I am trying to run molecular dynamics of ligand docked into the protein.
I have prepared the *.top and *.crd files. However, whaen I run the sander
it stops abruptly with the following error (for minimisation & molecular
dynamics both ).
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libc.so.6 00489410 Unknown Unknown Unknown
libc.so.6 0048AF81 Unknown Unknown Unknown
sander 08754169 Unknown Unknown Unknown
sander 0872C08D Unknown Unknown Unknown
sander 0872F1A7 Unknown Unknown Unknown
libpthread.so.0 0011C7C0 Unknown Unknown Unknown
sander 083B2A92 Unknown Unknown Unknown
sander 0812B671 Unknown Unknown Unknown
sander 081192ED Unknown Unknown Unknown
sander 08115C95 Unknown Unknown Unknown
sander 0804B1F5 Unknown Unknown Unknown
libc.so.6 0043BE23 Unknown Unknown Unknown
sander 0804B131 Unknown Unknown Unknown
My input file is
m8-minisation
&cntrl
imin=1, maxcyc =500,
ncyc = 250, ntb = 0, ntpr =1,
igb = 0, cut = 12,
/
The output file shows following lines
NSTEP ENERGY RMS GMAX NAME NUMBER
1 NaN NaN 7.0438E+08 HE1 4173
BOND = 512.6780 ANGLE = NaN DIHED = 3135.6235
VDWAALS = 70560903.2313 EEL = -20856.2773 HBOND = 0.0000
1-4 VDW = 2043.2988 1-4 EEL = 14310.2031 RESTRAINT = 0.0000
NSTEP ENERGY RMS GMAX NAME NUMBER
2 NaN NaN 0.0000E+00 N 1
BOND = NaN ANGLE = NaN DIHED = NaN
VDWAALS = 0.0000 EEL = 0.0000 HBOND = 0.0000
1-4 VDW = NaN 1-4 EEL = NaN RESTRAINT = 0.0000
I had tried different value of cutoff and ntpr, but all gave the same
result. I cannot understand what the problem is. Please suggest me some
solution to this problem
thanks in advance
-John
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Received on Fri Dec 12 2008 - 01:10:18 PST
