I met a problem with DECLARE of TORSION. Here is my input and output
results:
INPUT file:
-------------------
FILES_IN
# Input the parm.top file, and the coordinates.
PARM p1 CMV_Mono.top;
STREAM s1 CMVMono_CnsP_50_500ps_mdcrd.Z
CMVMono_CnsP_500_1ns_mdcrd.Z
CMVMono_CnsP_1_1.5ns_mdcrd.Z
CMVMono_CnsP_1.5_2ns_mdcrd.Z
CMVMono_CnsP_2_2.5ns_mdcrd.Z
CMVMono_CnsP_2.5_3ns_mdcrd.Z
../CMVMono_CnsP_3_3.5ns_mdcrd
../CMVMono_CnsP_3.5_4ns_mdcrd
../CMVMono_CnsP_4_4.5ns_mdcrd;
FILES_OUT
# output the coordinates in OUTPUT
TABLE tab1 Tab_Tor_103_120_4.5ns.tab;
TABLE tab2 Tab_Tor_130_159_4.5ns.tab;
DECLARE
TORSION tor1 BACKBONE[95 112];
TORSION tor2 BACKBONE[122 151];
OUTPUT
TABLE tab1 tor1;
TABLE tab2 tor2;
END
--------------------
OUTPUR file:
- CARNAL -
AMBER 6.0
COORDINATE ANALYSIS
input Car_Tor_01_4.5ns.in
> FILES_IN
> # Input the parm.top file, and the coordinates.
> PARM p1 CMV_Mono.top;
Reading parm file (CMV_Mono.top)
parm: opening CMV_Mono.top
CMV_Mono.top title:
> STREAM s1 CMVMono_CnsP_50_500ps_mdcrd.Z
Using default parm (CMV_Mono.top) for STREAM s1
(box will be read from stream)
> CMVMono_CnsP_500_1ns_mdcrd.Z
> CMVMono_CnsP_1_1.5ns_mdcrd.Z
> CMVMono_CnsP_1.5_2ns_mdcrd.Z
> CMVMono_CnsP_2_2.5ns_mdcrd.Z
> CMVMono_CnsP_2.5_3ns_mdcrd.Z
> ../CMVMono_CnsP_3_3.5ns_mdcrd
> ../CMVMono_CnsP_3.5_4ns_mdcrd
> ../CMVMono_CnsP_4_4.5ns_mdcrd;
stream: opening CMVMono_CnsP_500_1ns_mdcrd.Z
stream: opening CMVMono_CnsP_1_1.5ns_mdcrd.Z
stream: opening CMVMono_CnsP_1.5_2ns_mdcrd.Z
stream: opening CMVMono_CnsP_2_2.5ns_mdcrd.Z
stream: opening CMVMono_CnsP_2.5_3ns_mdcrd.Z
stream: opening ../CMVMono_CnsP_3_3.5ns_mdcrd
stream: opening ../CMVMono_CnsP_3.5_4ns_mdcrd
stream: opening ../CMVMono_CnsP_4_4.5ns_mdcrd
stream: opening CMVMono_CnsP_50_500ps_mdcrd.Z
>
>
> FILES_OUT
> # output the coordinates in OUTPUT
> TABLE tab1 Tab_Tor_103_120_4.5ns.tab;
> TABLE tab2 Tab_Tor_130_159_4.5ns.tab;
>
> DECLARE
>
> TORSION tor1 BACKBONE[95 112];
TORSION tor1 BACKBONE[95 112];
..........................^
Error in Car_Tor_01_4.5ns.in line 22: Not an atom name (or anything else)
Last token was BACKBONE[95
----------------------
I have tried :
TORSION tor1 BACKBONE [95 112];
&
TORSION tor1 BACKBONE[95 [112]];
&
TORSION tor1 BACKBONE[RES 95 112];
&
TORSION tor1 BACKBONE[RES 95-112];
&
TORSION tor1 BACKBONE[95-112];
&
TORSION tor1 BACKBONE[95,112];
.......
They all donot work.
Does anybody have this experience? Thanks.
William
-------------------------
William Wei
Faculty of Pharmacy
19 Russell Street
Toronto, ON. M5S 2S2
Tel: 1-416-946-8469
Fax: 1-416-978-8511
Email: william_at_phm.utoronto.ca
william.wei_at_utoronto.ca
Received on Fri Feb 07 2003 - 10:20:37 PST
