On Fri, Apr 29, 2011 at 2:40 PM, sunita gupta <sunita.bio.gmail.com> wrote:
> If I am using ntb = 1, I am getting an error "IMIN=5 does not support
> periodic boundaries (ifbox>0, ntb>0)", hence I uesd ntb =0
>
Oh. I guess that was a change made to amber11.
> On Fri, Apr 29, 2011 at 5:56 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > If water and stuff is present, do you really want to be using ntb == 0?
> If
> > you just use ntb = 1, then you should get the necessary behavior without
> > having to center/image (moreover, you actually treat the long-range
> > electrostatics properly).
> >
> > HTH,
> > Jason
> >
> > On Fri, Apr 29, 2011 at 1:42 PM, sunita gupta <sunita.bio.gmail.com>
> > wrote:
> >
> > > Yeah, water is present and centering of mdcrd file has been done using
> > > ptraj.
> > >
> > > Thanks
> > >
> > > On Fri, Apr 29, 2011 at 5:09 PM, Adrian Roitberg <roitberg.qtp.ufl.edu
> > > >wrote:
> > >
> > > > I am assuming this was done with a water box ?
> > > > Try centering/imaging your molecule/box before using imin=5
> > > >
> > > > On 4/29/11 1:36 PM, sunita gupta wrote:
> > > > > Hello Everyone,
> > > > >
> > > > > I am having 5ns mdcrd file and I want to minimize it further with
> > > imin=5
> > > > for
> > > > > maxcyc=5000. But here I am getting the mdcrd file having only one
> > frame
> > > > and
> > > > > no rst file.
> > > > > The out file shows that it ran for one step, Can anyone help me
> with
> > > this
> > > > > error? I am using Amber10.
> > > > > *min.in file (minimization input file)*
> > > > > &cntrl
> > > > > imin = 5,
> > > > > maxcyc = 5000,
> > > > > ncyc = 2000,
> > > > > ntb = 0,
> > > > > ntr = 0,
> > > > > cut = 12, ntpr = 1, ntwx = 1,
> > > > > nmropt=0,
> > > > > /
> > > > > *Min.out file is pasted below:*
> > > > >
> > > > > Maximum number of minimization cycles reached.
> > > > > FINAL RESULTS
> > > > > NSTEP ENERGY RMS GMAX NAME
> > > > NUMBER
> > > > > 5000 -8.7965E+04 3.1104E+00 8.1496E+01 HB2
> 1765
> > > > >
> > > > > BOND = 13550.5326 ANGLE = 985.3458 DIHED =
> > > > > 3417.9826
> > > > > VDWAALS = 27007.4725 EEL = -149685.0349 HBOND =
> > > > > 0.0000
> > > > > 1-4 VDW = 1250.1481 1-4 EEL = 15508.2819 RESTRAINT =
> > > > > 0.0000
> > > > > minimization completed, ENE= -.87965271E+05 RMS= 0.311043E+01
> > > > > minimizing coord set # 2
> > > > > Frac coord min, max: -1202863.84373385 1202865.00693183
> > > > > The system has extended beyond
> > > > > the extent of the virtual box.
> > > > > Restarting sander will recalculate
> > > > > a new virtual box with 30 Angstroms
> > > > > extra on each side, if there is a
> > > > > restart file for this configuration.
> > > > > SANDER BOMB in subroutine Routine: map_coords (ew_force.f)
> > > > > Atom out of bounds. If a restart has been written,
> > > > > restarting should resolve the error
> > > > >
> > > > > *The command used is:* mpirun -np 4 /opt/apps/amber10/exe/sander -O
> > -i
> > > > > min.in -o LI4_min.out -p pro_LI4.top -c pro_LI4.crd -y
> LI4_5ns.mdcrd
> > > -r
> > > > > LI4_min.crd -x LI4_min.mdcrd
> > > > >
> > > >
> > > > --
> > > > Dr. Adrian E. Roitberg
> > > > Associate Professor
> > > > Quantum Theory Project, Department of Chemistry
> > > > University of Florida
> > > >
> > > > on Sabbatical in Barcelona until August 2011.
> > > > Email roitberg.ufl.edu
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > >
> > > --
> > > --
> > > SUNITA GUPTA
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> --
> SUNITA GUPTA
> Member Research Staff
> LeadInvent Technologies Pvt.Ltd
> Biotech Centre, University of Delhi
> South Campus, Benito Juarez Road,
> New Delhi, Pin 110021
> Email- sunita.leadinvent.com
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Apr 29 2011 - 06:00:04 PDT
