Dear amber users,
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 &endRestarints25.0RES 1 338ENDEND
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.
Best Regards, Saman Yousuf AliJunior Research Fellow,
| Lab No. P-133, Computational Chemistry Laboratory
Dr. Panjwani Center for Molecular Medicine & Drug Research,
International Center for Chemical & Biological Sciences,
University of Karachi – 75270.Karachi-Pakistan.
Contact No:
Office (92-21) 111222292 (Ext 309)
Email ID: saman.yousufali64.yahoo.com
saman.ali.iccs.edu
|
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jan 24 2016 - 02:00:03 PST
