Re: [AMBER] Restrain a single atom in the residue during minimization, instead of all the atoms in a residue with RES option

From: Vasantha Kumar <vin.vasanth.gmail.com>
Date: Tue, 10 May 2016 10:32:54 +0200

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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>


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Received on Tue May 10 2016 - 02:00:03 PDT
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