I'm getting a "segmentation fault" when I run the following command:
----------------
sander -O -i md.belly.in -o md.belly.out -p polyAT.prmtop -c
min.belly.restart -r md.belly.restart -x md.belly.traj &
----------------
The input file is:
----------
5DNB, initial dynamics w/ belly on DNA, model1, 9.0 cut
&cntrl
ntpr = 10, ntwx = 500,
ntf = 2, ntb = 2,
cut = 9.0,
ibelly = 1,
nstlim = 12500,
nscm = 0,
dt = 0.002,
temp0 = 300.0, tempi = 100.0,
ntt = 1,
tautp = 0.2,
ntp = 1,
ntc = 2, tol = 0.0005,
&end
&wt
type='TEMP0', istep1=0, istep2=500,
value1=100.0, value2=300.0,
&end
&wt
type='TEMP0', istep1=500, istep2=12500,
value1=300.0, value2=300.0,
&end
&wt
type='END',
&end
&rst
iat=0,
&end
Allowing only the water and counterions to move in the belly
RES 21 3547
END
END
----------
and the output file (before it crashes, anyway) is (note the excess
spaces at the end):
----------
-------------------------------------------------------
Amber 7 SANDER Scripps/UCSF 2002
-------------------------------------------------------
| Thu Oct 17 14:18:51 2002
[-O]verwriting output
File Assignments:
| MDIN: md.belly.in
| MDOUT: md.belly.out
|INPCRD: min.belly.restart
| PARM: polyAT.prmtop
|RESTRT: md.belly.restart
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: md.belly.traj
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
5DNB, initial dynamics w/ belly on DNA, model1, 9.0 cut
&cntrl
ntpr = 10, ntwx = 500,
ntf = 2, ntb = 2,
cut = 9.0,
ibelly = 1,
nstlim = 12500,
nscm = 0,
dt = 0.002,
temp0 = 300.0, tempi = 100.0,
ntt = 1,
tautp = 0.2,
ntp = 1,
ntc = 2, tol = 0.0005,
&end
&wt
type='TEMP0', istep1=0, istep2=500,
value1=100.0, value2=300.0,
&end
&wt
type='TEMP0', istep1=500, istep2=12500,
value1=300.0, value2=300.0,
&end
&wt
type='END',
&end
&rst
iat=0,
----------
Can anyone see what's causing this?
- Joel
Received on Thu Oct 17 2002 - 12:28:48 PDT
