I don't see the refc defined in your script. Is this the first minimization
step? Did you put the reference coordinates in the min1? Check the manual
for details.
On May 10, 2016 4:33 AM, "Vasantha Kumar" <vin.vasanth.gmail.com> wrote:
> Dear Carlos and amber users
>
> Please find the attachment of the min2 output file. In the output file it
> stopped as follows.
>
> error(detail file is attached):
>
> LOADING THE CONSTRAINED ATOMS AS GROUPS
> 5. REFERENCE ATOM COORDINATES
> Error opening unit 10: File "refc" is missing or unreadable
>
>
>
> command used
> sander -O -i min2.in -o Peptide_ZAFF_solvate_min2.out -p
> Peptide_ZAFF_solvate.prmtop -c Peptide_ZAFF_solvate_min1.rst -r
> Peptide_ZAFF_solvate_min2.rst -x Peptide_ZAFF_solvate_min2.mdcrd
>
> thanks in advance
> Vince
>
> On Mon, May 9, 2016 at 10:34 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > you haven't shown us your script, but a good place to start is with the
> > error message, that your refcfile is missing.
> >
> > On Mon, May 9, 2016 at 4:32 PM, Vasantha Kumar <vin.vasanth.gmail.com>
> > wrote:
> >
> > > Dear AMBER user
> > >
> > > I want to minimize structure in TIP3PBOX in two state (min1.in and
> > min2.in
> > > || input files below).
> > > In particular I want to minimize my molecule where zinc coordinated
> atoms
> > > (SG of CYS and NE2 of HIS and ZN of Zinc) in the restrained or freeze
> > mode
> > > so that I can save my metal geometry. min1.in runs fine but for
> min2.in
> > > there is an error with ntr=1. Im not able to launch minimization. it
> says
> > > rfec file is missing or not readable. Im using amber 12.
> > >
> > > I used following style or definition to restrain single atom in 4
> > different
> > > residues instead of all the atom in the single residue.
> > >
> > > min2.in
> > > .
> > > .
> > > .
> > > .
> > >
> > > Group input for restrained atoms
> > > 500.0
> > > RES 4.SG, 7.SG, 19.NE2, 22.NE2, 26.ZN
> > >
> > > so I am not sure is it correct way to define just to restrain single
> atom
> > > in 4 different residues as 4.SG, 7.SG, 19.NE2, 22.NE2, 26.ZN
> > >
> > > if any one know to restrain single atom please suggest me
> > >
> > > thanks in advance
> > > Vince
> > >
> > > PS : the files that I using to minimization
> > >
> > > min1.in
> > > =========
> > > Peptide : minimisation solvent+ions with molecule fided
> > > &cntrl
> > > imin = 1,
> > > maxcyc = 10000,
> > > ncyc = 5000,
> > > ntb = 1,
> > > ntr = 1,
> > > cut = 10.0,
> > > ntpr = 50,
> > > ntwx = 50
> > > /
> > > Hold Peptide_solvate fixed
> > > 500.0
> > > RES 1 26
> > > END
> > > END
> > >
> > >
> > > min2.in
> > > ========
> > > Peptide : minimisation entire system
> > > &cntrl
> > > imin = 1,
> > > maxcyc = 2500,
> > > ncyc = 1000,
> > > ntb = 1,
> > > ntr = 1,
> > > cut = 10.0,
> > > ntpr = 50,
> > > ntwx = 50
> > > /
> > > Group input for restrained atoms
> > > 500.0
> > > RES 4.SG, 7.SG, 19.NE2, 22.NE2, 26.ZN
> > > END
> > > END
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
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> >
>
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Received on Tue May 10 2016 - 03:00:04 PDT
