Dear Amber users
I am doing minimization of protein ligand complex in amber with restraint
on heavy atoms except water and hydrogen
At first I keep ncyc =100 as follows
imin=1,
irest=0, ntx=1,
maxcyc=10000, *ncyc=100*,
ntpr=50,
cut=10.0,
ntb=2, ntp=1,
ntr=1,
restraintmask= '(:* & !.H=) &!(.WAT | .Na+=)',
restraint_wt=50,
&end
END
However I get error of LINMIN FAILURE as follows
NSTEP ENERGY RMS GMAX NAME NUMBER
3600 -5.0525E+05 7.6371E-03 1.2839E+00 C7N 7936
BOND = 28632.8041 ANGLE = 1059.3257 DIHED =
6086.7976
VDWAALS = 41556.3339 EEL = -609017.9500 HBOND =
0.0000
1-4 VDW = 2087.7003 1-4 EEL = 18090.7900 RESTRAINT =
6255.2630
EAMBER = -511504.1985
... *RESTARTED DUE TO LINMIN FAILURE* ...
NSTEP ENERGY RMS GMAX NAME NUMBER
3650 -5.0525E+05 3.6128E-03 1.2359E+00 CG 2815
BOND = 28632.8294 ANGLE = 1059.3316 DIHED =
6086.8292
VDWAALS = 41556.4329 EEL = -609018.3013 HBOND =
0.0000
1-4 VDW = 2087.7014 1-4 EEL = 18090.8174 RESTRAINT =
6255.2880
EAMBER = -511504.3594
... RESTARTED DUE TO LINMIN FAILURE ...
***** REPEATED LINMIN FAILURE *****
***** SEE
http://ambermd.org/Questions/linmin.html FOR MORE INFO *****
As per suggested in
http://ambermd.org/Questions/linmin.html
I increased *ncyc =1000*
I am getting same error at 4500 steps
NSTEP ENERGY RMS GMAX NAME NUMBER
4500 -5.0525E+05 2.0544E-03 7.2654E-01 H1 49141
BOND = 28632.9335 ANGLE = 1059.6083 DIHED =
6087.0660
VDWAALS = 41556.1526 EEL = -609020.2894 HBOND =
0.0000
1-4 VDW = 2087.6859 1-4 EEL = 18090.4382 RESTRAINT =
6256.1539
EAMBER = -511506.4049
... *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
4513 -5.0525E+05 2.0137E-03 7.1968E-01 H1 49141
BOND = 28632.9335 ANGLE = 1059.6083 DIHED =
6087.0661
VDWAALS = 41556.1527 EEL = -609020.2893 HBOND =
0.0000
1-4 VDW = 2087.6858 1-4 EEL = 18090.4379 RESTRAINT =
6256.1539
EAMBER = -511506.4051
Can anyone please suggest me the solution?
Thank you
Sadaf
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Received on Thu Jun 27 2019 - 09:00:04 PDT
