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 Thu Nov 16 2000 - 08:13:48 PST
