Hello
This is ok.
just that minimizer could not search any more conformation lower than the present ones.
The link that you added with this says the following on this
The LINMIN failures occur frequently when performing minimization. They don't mean that any sort of evil failure of minimization has occurred, only that the minimizer got "stuck" in a place from which the minimization algorithm could not find a way out. Unless there is something very askew with your system, the amount of minimization that has occurred by the time you reach such a "sticking" point will be sufficient to move on to MD or Gibbs. (It wouldn't be sufficient to carry out a normal modes calculation, but a different minimizer is used then, anyway).
Best Regards
Elvis Martis
________________________________
From: Sadaf Rani <sadafrani6.gmail.com>
Sent: 27 June 2019 21:26
To: AMBER Mailing List
Subject: [AMBER] RESTARTED DUE TO LINMIN FAILURE
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 - 09:30:02 PDT
