AMBER Archive (2003)

Subject: AMBER: Freezing the residues

From: Vikas Varshney (vikas_var_at_rediffmail.com)
Date: Thu Oct 09 2003 - 22:37:11 CDT

Hi Amber Users, Thanks Scott and Asim for answering my query. I got restrt file now. I want to freeze some of my residues during 'minimization'. What should I do. I tried to use RES in input file for sanders with force constant value 2 but the atom moved a lot after the minimzation. Should I use higher value of force constant like 100 or am I missing something. I will appreciate if you can answer my queries. Thanks & regards, VIkas Varshney Dept. of polymer science University of Akron. On Fri, 10 Oct 2003 Scott Brozell wrote : >Hello, > >ntwr applies to dynamics not minimization. >A restart file is written every NSTLIM steps for both >dynamics and minimization. > >When I tried your input, after decreasing the surprisingly large >maxcyc to 700, using the prmtop and inpcrd from test/ubiquitin, >a restart file was written at step 700. >Without knowing the details of your system it is recommended >that maxcyc be reduced by a couple of orders of magnitude. > >Scott > >On Thu, 9 Oct 2003, Asim Okur wrote: > > > To be able to write a restrt file you have to use ntwr in the input > > file. > > > > ntwr = 10 > > > > will write to the restart file every 10 steps, > > > > Asim Okur > > > > > > > > -----Original Message----- > > From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf > > Of Vikas Varshney > > Sent: Thursday, October 09, 2003 5:40 PM > > To: amber_at_scripps.edu > > Subject: AMBER: Not getting restrt file on running sanders > > > > Dear AMBER users, > > I tried to run minimization of a system of around 500 residues (~5000 > > atoms) in > > sander with option -r restart, but did not get the restart file. Here is > > my input file. > > Minimization > > &cntrl > > imin=1,maxcyc=100000,ntmin=2, > > ntpr=10,iwrap=1, > > &end > > Group input for restrained atoms > > 2.0 > > RES 383 478 > > END > > END > > > > I will really appreciate if you are can help me with this. > > > > Many regards and thanks, > > > > VIkas Varshney > > Dept. of polymer science > > University of Akron. > > > > > > <http://clients.rediff.com/signature/track_sig.asp> > > > >----------------------------------------------------------------------- >The AMBER Mail Reflector >To post, send mail to amber_at_scripps.edu >To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu >

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