AMBER Archive (2003)

Subject: Re: Carnal DECLARE of TORSION problem

From: Holger Gohlke (gohlke_at_scripps.edu)
Date: Fri Feb 07 2003 - 12:34:07 CST

Hi,

in the torsion command "TORSION id BACKBONE [res1 [res2]];", the
brackets just denote that the input of res1/res2 is optional.
So try "TORSION t1 BACKBONE 95 112;" below.

Best regards

Holger

> 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 

-- 
+++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
Dept. of Molecular Biology, TPC15
The Scripps Research Institute
10550 N. Torrey Pines Rd.
La Jolla CA 92037  USA
phone: +1-858-784-9788
fax:   +1-858-784-8896
email: gohlke_at_scripps.edu
+++++++++++++++++++++++++++++++++++++++++++++