Dear all,
I am trying to get the ras-raf tutorial work for the MMPBSA tutorial. And
basically I am having problem at the very first minimization step.
Initially I used maxcyc=1000 and ncyc=500 and I kept getting " ...
RESTARTED DUE TO LINMIN FAILURE ...
" message exactly after 500 steps i.e when its suppose to switch from SD to
CD.It does that everything right when it is supposed to make that switch
from SD to CD irrespective whaat the ncyc and maxcyc are. I looked up
online for some suggestions and I increased the ncyc but still got the same
error. Next I tried to go higher number of cycles and higher ncyc but again
the same problem. I tried with my own protein system and still got the same
error. I wonder why I am getting this problem even though I am just trying
to replicate the tutorial already given here? I haven't changed anything.
Any suggestions would be very helpful as I am stuck with this error in very
first step. Greatly appreciate your time and concern in this regard.
minimise ras-raf
&cntrl
imin=1,maxcyc=50000,ncyc=25000,
cut=8.0,ntb=1,
ntc=2,ntf=2,
ntpr=100,
ntr=1, restraintmask=':1-242',
restraint_wt=2.0
/
Min_out: (First few steps)
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -1.1557E+05 1.5813E+01 1.0134E+02 N 3050
BOND = 668.3731 ANGLE = 1977.0327 DIHED =
3166.3187
VDWAALS = 11017.1290 EEL = -141676.9599 HBOND =
0.0000
1-4 VDW = 853.0247 1-4 EEL = 8429.1551 RESTRAINT =
0.0009
EAMBER = -115565.9266
NSTEP ENERGY RMS GMAX NAME NUMBER
100 -1.2212E+05 1.3808E+01 4.4788E+01 O 35909
BOND = 161.4912 ANGLE = 667.7441 DIHED =
2927.2817
VDWAALS = 6113.9242 EEL = -141292.2411 HBOND =
0.0000
1-4 VDW = 768.2178 1-4 EEL = 8495.9778 RESTRAINT =
34.7033
EAMBER = -122157.6044
NSTEP ENERGY RMS GMAX NAME NUMBER
200 -1.2212E+05 1.3808E+01 4.4788E+01 O 35909
BOND = 161.4910 ANGLE = 667.7436 DIHED =
2927.2815
VDWAALS = 6113.9134 EEL = -141292.2188 HBOND =
0.0000
1-4 VDW = 768.2177 1-4 EEL = 8495.9777 RESTRAINT =
34.7034
EAMBER = -122157.5938
NSTEP ENERGY RMS GMAX NAME NUMBER
300 -1.2212E+05 1.3808E+01 4.4788E+01 O 35909
BOND = 161.4909 ANGLE = 667.7431 DIHED =
2927.2813
VDWAALS = 6113.9026 EEL = -141292.1948 HBOND =
0.0000
1-4 VDW = 768.2177 1-4 EEL = 8495.9776 RESTRAINT =
34.7035
EAMBER = -122157.5816
(Last few steps)
NSTEP ENERGY RMS GMAX NAME NUMBER
25000 -1.2212E+05 1.3807E+01 4.4781E+01 O 35909
BOND = 161.4651 ANGLE = 667.6073 DIHED =
2927.2358
VDWAALS = 6111.2733 EEL = -141286.1207 HBOND =
0.0000
1-4 VDW = 768.2016 1-4 EEL = 8495.9983 RESTRAINT =
34.7331
EAMBER = -122154.3392
... RESTARTED DUE TO LINMIN FAILURE ...
... RESTARTED DUE TO LINMIN FAILURE ...
... RESTARTED DUE TO LINMIN FAILURE ...
... RESTARTED DUE TO LINMIN FAILURE ...
NSTEP ENERGY RMS GMAX NAME NUMBER
25100 -1.2212E+05 1.3807E+01 4.4781E+01 O 35909
BOND = 161.4651 ANGLE = 667.6072 DIHED =
2927.2358
VDWAALS = 6111.2702 EEL = -141286.1127 HBOND =
0.0000
1-4 VDW = 768.2016 1-4 EEL = 8495.9983 RESTRAINT =
34.7332
EAMBER = -122154.3345
... RESTARTED DUE TO LINMIN FAILURE ...
***** REPEATED LINMIN FAILURE *****
***** SEE
http://ambermd.org/Questions/linmin.html FOR MORE INFO *****
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
25114 -1.2212E+05 1.3807E+01 4.4781E+01 O 35909
BOND = 161.4651 ANGLE = 667.6071 DIHED =
2927.2358
VDWAALS = 6111.2698 EEL = -141286.1117 HBOND =
0.0000
1-4 VDW = 768.2016 1-4 EEL = 8495.9983 RESTRAINT =
34.7332
EAMBER = -122154.3340
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Mar 01 2016 - 15:00:03 PST
