AMBER Archive (2000)

Subject: (no subject)

From: Joseph Nachman (nachman_at_hera.med.utoronto.ca)
Date: Thu Nov 16 2000 - 10:13:48 CST

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
--------------------------------------------------------------------