Dear Martis
May be I am asking a more silly question but I am in learning phase sorry
If I put some odd question. Can you please ellaborate a little bit
regarding normal mode calculation and use of different minimizer? Here I am
just doing energy minimization what else about minimization
Also how can I get the plot of minimization output file
(complex_water-2.out in my case) ploting energy vs no of steps in order to
visualise.
command grep ENERGY complex_water-2.out | awk '{print$1,$3} > Energy.dat
not working is there ant mistake in it?
thank you
Sadaf
On Thu, Jun 27, 2019 at 5:24 PM Elvis Martis <elvis.martis.bcp.edu.in>
wrote:
> 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 27 2019 - 11:00:02 PDT
