RE: AMBER: forrtl severe(174) error with minimization and md

From: Ross Walker <>
Date: Wed, 10 Dec 2008 07:57:42 -0800

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



From: [] 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 00489410 Unknown Unknown Unknown 0048AF81 Unknown Unknown Unknown

sander 08754169 Unknown Unknown Unknown

sander 0872C08D Unknown Unknown Unknown

sander 0872F1A7 Unknown Unknown Unknown 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 0043BE23 Unknown Unknown Unknown

sander 0804B131 Unknown Unknown Unknown

My input file is



imin=1, maxcyc =500,

ncyc = 250, ntb = 0, ntpr =1,

igb = 0, cut = 12,


The output file shows following lines


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



2 NaN NaN 0.0000E+00 N 1


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


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Received on Fri Dec 12 2008 - 01:10:18 PST
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