Dear all,
I am a beginner at amber and I have some troubles in understanding, amber minimization input file flags. I am using the following script for minimzation,
Minimization Amber12
&cnrl
imin=1, maxcyc=1000, ntmin = 2,
ntx = 1, ntc =1, ntf = 1,
ntb =1, ntp = 0, ncyc = 100,
ntwx = 1000, ntwe = 0, ntpr = 1000,
ntr = 1, cut = 10.0
&end
Restarints
25.0
RES 1 338
END
END
Here in above input file, I write maxcyc 1000 with restraint of 25 KCal/mol, is applied on protein and then minimization is followed by gradually relaxing restraints on both protein and counter ions (20,15,10,5) and then unrestraint.
Kindly tell me, total number of minimization steps carried out by using these input files are 6000 0r 2000? Also tell me if ncyc > maxcyc, like maxcyc is 1000 and ncyc is 5000, what does it mean?
Thanks you.
First step is to do the AMBER tutorials.
Then, search the manual for the flag (e.g. ncyc) you wish to learn about.
If you are still stuck, you'll get better/faster responses if you sign up and ask questions on the mailing list:
http://lists.ambermd.org/mailman/listinfo/amber
The input file does not do what you say it does re relaxing restraints
ncyc specifies when to switch from steepest decent to conjugate gradient. But you have ntmin = 2, so only SD will be performed and ncyc will be ignored.
maxcyc is max number of steps/cycles to perform. So if it has not yet reached a minimum by maxcyc, it will stop.
Dear Olive,
Thank you for your response. I will follow your suggestions.
- Badges
- Science method