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
>
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>
--
--
SUNITA GUPTA
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Received on Fri Apr 29 2011 - 05:00:04 PDT
