Dear Dr. Nachman,
I am not sure whether the force constant (below the command "SEARCH")
is formatted or free-field input, but the only suggestion I would have
is to remove one space before the first such constant (100.0) since I
noticed that the next two constants have the decimal point one space
further left than this first one. Other than this I don't notice any
errors in the input,
but I'll have a closer look at the file when I get a chance.
Good luck.
Sincerely,
Michael G. Cooney
Department of Biochemistry and Molecular Biology
The University of Georgia
Athens, GA 30602
On Thu, 16 Nov 2000, Joseph Nachman wrote:
> Hello AMBER users,
>
> I'm trying to run a simmulated annealing in vacuum using sander-classic,
> in which I'm trying to apply different restraints to backbone and side
> chain in a part of my protein; basically I'm trying to fix the
> main-chain, while allowing more freedom to the side chains. Uding the
> exmples in the section on group definitions in the manual as a guide I'm
> tryin g to define the groups targeted for restrains:
>
> ------------------------------------------------------------------------
>
> Simmulated annealing
> &cntrl
> imin=0, irest=0, ntx=1,
> ntt=1, tempi=0., temp0=5000., tautp=2.0,
> ntb=0, ntr=1, scee=1.2,
> ntc=2, tol=0.00001, dt=0.002, ntf=2, ntcm=1,
> nstlim=25000, ntwx=500, ntpr=500,
> &end
> Fix protein backbone:
> FIND
> * * M *
> * H E *
> * O E *
> SEARCH
> 100.0
> RES 101 107
> END
> Harmonically restrain sidechains:
> FIND
> * * S *
> * * B *
> * * 3 *
> * * E *
> SEARCH
> 10.0
> ((RES 1 7) & (9 27) & (29 100))
> END
> Harmonically restrain sidechains:
> FIND
> * * S *
> * * B *
> * * 3 *
> * * E *
> SEARCH
> 25.0
> ((RES 8) & (RES 28) & (RES 104))
> END
> END
>
> --------------------------------------------------------------------
>
> However, AMBER doesn't seem to recognize my variables in the group
> definitions:
>
> -------------------------------------------------------------------
>
>
> -------------------------------------------------------
> Amber 6 SANDER_CLASSIC Scripps/UCSF 1999
> -------------------------------------------------------
>
> | Tue Nov 14 16:32:43 2000
>
> [-O]verwriting output
>
> File Assignments:
> |MDIN : sa2.in
> |MDOUT: sa2.out
> |INPCR: min.xyz
> |PARM : /disk1/nachman/yeei.top
> |RESTR: sa2.xyz
> |REFC : min.xyz
> |MDVEL: mdvel
> |MDEN : mden
> |MDCRD: sa2.crd
> |MDINF: mdinfo
>
>
> Here is the input file:
>
> Simmulated annealing
> &cntrl
> imin=0, irest=0, ntx=1,
> ntt=1, tempi=0., temp0=5000., tautp=2.0,
> ntb=0, ntr=1, scee=1.2,
> ntc=2, tol=0.00001, dt=0.002, ntf=2, ntcm=1,
> nstlim=25000, ntwx=500, ntpr=500,
> &end
> Fix protein backbone:
> FIND
> * * M *
> * H E *
> * O E *
> SEARCH
> 100.0
> RES 101 107
> END
> Harmonically restrain sidechains:
> FIND
> * * S *
> * * B *
> * * 3 *
> * * E *
> SEARCH
> 10.0
> ((RES 1 7) & (9 27) & (29 100))
> END
> Harmonically restrain sidechains:
> FIND
> * * S *
> * * B *
> * * 3 *
> * * E *
> SEARCH
> 25.0
> ((RES 8) & (RES 28) & (RES 104))
> END
> END
> -------------------------------------------------------------------------------
>
> Simulated annealing
>
> | Reading &cntrl namelist w/ machine lib
>
> [...snip...]
>
> Water definition for fast triangulated model:
> Resname = WAT ; Oxygen_name = O ; Hyd1_name = H1 ; Hyd2_name = H2
>
> GFTIM = 2.00000 RLMAVF= 0.00000 ISGDEP= 3
> NMRAFA= 0 ILTAVF= 0
>
> LOADING THE CONSTRAINED ATOMS AS GROUPS
>
>
> 5. REFERENCE ATOM COORDINATES
>
>
> ----- READING GROUP 1; TITLE:
> Fix protein backbone:
>
> rfree: Error decoding variable 1 3 from:
> FIND
>
> --------------------------------------------------------------------
>
> Any ideas?
>
> Thanks in advance,
>
> Joseph Nachman
>
> --------------------------------------------------------------------
> Joseph Nachman Department of Biochemistry
> nachman_at_hera.med.utoronto.ca University of Toronto
> Medical Sciences Building
> tel: +1 416 978-5510 Toronto, Ontario M5S 1A8
> fax: +1 416 978-8548 Canada
> --------------------------------------------------------------------
>
Received on Fri Nov 17 2000 - 08:56:30 PST
