Dear Carlos
I have figure out the problem associate with missing refc file, now I can
launch minimization.
Now I am wondering that the definition that I used to restrain specific
atom in a residue is correct?
I would highly appreciate your answer..
thanks in advance
Vince
On Tue, May 10, 2016 at 10:32 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
>> > _______________________________________________
>> > 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 - 02:30:05 PDT
