Hi,
I am using Amber11 to run simulation of a protein system. During
equilibration, I wanted to restrain the protein and let the water molecules
to relax. The simulation crashed with the error messege:
At line 390 of file _set.f
Fortran runtime error: Bad value during integer read
And the last thing printed out in the mdout file is:
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
My mdin has the following parameters for the restraint:
ntr=1,restraint_wt=5.0, restraintmask='.1-1602'
Line 390 of the _set.f is as follows:
if( line(6:6) == ' ' ) then ! this is an old, i5 file
read(line,'(i5)') natom
It seems it is having problem reading the number of atoms from the refc
file, THe refc file I used has the same format as restrt, which looks like
this:
%VERSION VERSION_STAMP = V0001.000 DATE = 11/10/10 22:36:28
%FLAG TITLE
%FORMAT(a)
mut-wat
%FLAG ATOMIC_COORDS_SIMULATION_TIME
%FORMAT(E16.8)
0.00000000E+00
%FLAG ATOMIC_COORDS_NUM_LIST
%FORMAT(i8)
8565
%FLAG ATOMIC_COORDS_LIST
%COMMENT dimension = (3,8565)
%FORMAT(3e20.12)
-0.766903000000E+01 0.112542130000E+02 0.696263600000E+01
-0.671903000000E+01 0.102182130000E+02 0.734463600000E+01
-0.538203000000E+01 0.104392130000E+02 0.665163600000E+01
-0.529103000000E+01 0.111622130000E+02 0.566163600000E+01
-0.794603000000E+01 0.111262130000E+02 0.600663600000E+01
What did I do wrong with the restraint?
Thanks
Dian
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 15 2010 - 14:30:05 PST
