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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Received on Mon May 09 2016 - 14:00:04 PDT
