AMBER Archive (2003)

Subject: Carnal DECLARE of TORSION problem

From: William Wei (william.wei_at_utoronto.ca)
Date: Fri Feb 07 2003 - 12:20:37 CST

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