AMBER Archive (2007)

Subject: AMBER: Problem in running CARNAL

From: Vijay Manickam Achari (vjrajamany_at_yahoo.com)
Date: Thu Dec 06 2007 - 23:52:26 CST


Dear sir,
I have sent my CARNAL input file here.
You can have a look on this.
For your information I am using AMBER 7 which contains
CARNAL. Thank you sir.

 my CARNAL script is as below:
 
 FILES_IN
    PARM p1 betaM_lyo.top;
    STREAM s1 betaM_lyo_md02_0100.mdcrd.gz;
 
 FILES_OUT
    HBOND h1 xhb TABLE LIST;
    HBOND h2 xhb TABLE LIST;
    HBOND h3 xhb TABLE LIST;
    HBOND h4 xhb TABLE LIST;
    HBOND h5 xhb TABLE LIST;
    HBOND h6 xhb TABLE LIST;
    HBOND h7 xhb TABLE LIST;
    HBOND h8 xhb TABLE LIST;
    HBOND h9 xhb TABLE LIST;
    HBOND h10 xhb TABLE LIST;
 
    HBOND h11 xhb TABLE LIST;
    HBOND h12 xhb TABLE LIST;
    HBOND h13 xhb TABLE LIST;
    HBOND h14 xhb TABLE LIST;
    HBOND h15 xhb TABLE LIST;
    HBOND h16 xhb TABLE LIST;
    HBOND h17 xhb TABLE LIST;
    HBOND h18 xhb TABLE LIST;
    HBOND h19 xhb TABLE LIST;
    HBOND h20 xhb TABLE LIST;
 
    HBOND h21 xhb TABLE LIST;
    HBOND h22 xhb TABLE LIST;
    HBOND h23 xhb TABLE LIST;
    HBOND h24 xhb TABLE LIST;
    HBOND h25 xhb TABLE LIST;
    HBOND h26 xhb TABLE LIST;
    HBOND h27 xhb TABLE LIST;
    HBOND h28 xhb TABLE LIST;
    HBOND h29 xhb TABLE LIST;
    HBOND h30 xhb TABLE LIST;
 
    HBOND h31 xhb TABLE LIST;
    HBOND h32 xhb TABLE LIST;
    HBOND h33 xhb TABLE LIST;
    HBOND h34 xhb TABLE LIST;
    HBOND h35 xhb TABLE LIST;
    HBOND h36 xhb TABLE LIST;
    HBOND h37 xhb TABLE LIST;
    HBOND h38 xhb TABLE LIST;
    HBOND h39 xhb TABLE LIST;
    HBOND h40 xhb TABLE LIST;
 
    HBOND h41 xhb TABLE LIST;
    HBOND h42 xhb TABLE LIST;
    HBOND h43 xhb TABLE LIST;
    HBOND h44 xhb TABLE LIST;
    HBOND h45 xhb TABLE LIST;
    HBOND h46 xhb TABLE LIST;
    HBOND h47 xhb TABLE LIST;
    HBOND h48 xhb TABLE LIST;
    HBOND h49 xhb TABLE LIST;
    HBOND h50 xhb TABLE LIST;
 
    HBOND h51 xhb TABLE LIST;
    HBOND h52 xhb TABLE LIST;
    HBOND h53 xhb TABLE LIST;
    HBOND h54 xhb TABLE LIST;
    HBOND h55 xhb TABLE LIST;
    HBOND h56 xhb TABLE LIST;
    HBOND h57 xhb TABLE LIST;
    HBOND h58 xhb TABLE LIST;
    HBOND h59 xhb TABLE LIST;
    HBOND h60 xhb TABLE LIST;
 
 
    HBOND h61 xhb TABLE LIST;
    HBOND h62 xhb TABLE LIST;
    HBOND h63 xhb TABLE LIST;
    HBOND h64 xhb TABLE LIST;
    HBOND h65 xhb TABLE LIST;
    HBOND h66 xhb TABLE LIST;
    HBOND h67 xhb TABLE LIST;
    HBOND h68 xhb TABLE LIST;
    HBOND h69 xhb TABLE LIST;
    HBOND h70 xhb TABLE LIST;
 
 
 DECLARE
 
    GROUP g1 ((ATOM NAME O12) & ( RES 1));
    GROUP g2 ((ATOM NAME O11) & ( RES 1));
    GROUP g3 ((ATOM NAME O13) & ( RES 1));
    GROUP g4 ((ATOM NAME O15) & ( RES 1));
    GROUP g5 ((ATOM NAME O16) & ( RES 1));
    GROUP g6 ((ATOM NAME O14) & ( RES 1));
    GROUP g7 ((ATOM NAME O22) & ( RES 1));
    GROUP g8 ((ATOM NAME O23) & ( RES 1));
    GROUP g9 ((ATOM NAME O24) & ( RES 1));
    GROUP g10 ((ATOM NAME O25) & ( RES 1));
    GROUP g11 ((ATOM NAME O26) & ( RES 1));
 
    GROUP g12 ((ATOM NAME O13) & ( RES 1));
    GROUP g13 ((ATOM NAME O11) & ( RES 1));
    GROUP g14 ((ATOM NAME O12) & ( RES 1));
    GROUP g15 ((ATOM NAME O15) & ( RES 1));
    GROUP g16 ((ATOM NAME O16) & ( RES 1));
    GROUP g17 ((ATOM NAME O14) & ( RES 1));
    GROUP g18 ((ATOM NAME O22) & ( RES 1));
    GROUP g19 ((ATOM NAME O23) & ( RES 1));
    GROUP g20 ((ATOM NAME O24) & ( RES 1));
    GROUP g21 ((ATOM NAME O25) & ( RES 1));
    GROUP g22 ((ATOM NAME O26) & ( RES 1));
 
    GROUP g23 ((ATOM NAME O16) & ( RES 1));
    GROUP g24 ((ATOM NAME O11) & ( RES 1));
    GROUP g25 ((ATOM NAME O12) & ( RES 1));
    GROUP g26 ((ATOM NAME O13) & ( RES 1));
    GROUP g27 ((ATOM NAME O15) & ( RES 1));
    GROUP g28 ((ATOM NAME O14) & ( RES 1));
    GROUP g29 ((ATOM NAME O22) & ( RES 1));
    GROUP g30 ((ATOM NAME O23) & ( RES 1));
    GROUP g31 ((ATOM NAME O24) & ( RES 1));
    GROUP g32 ((ATOM NAME O25) & ( RES 1));
    GROUP g33 ((ATOM NAME O26) & ( RES 1));
 
    GROUP g34 ((ATOM NAME O22) & ( RES 1));
    GROUP g35 ((ATOM NAME O11) & ( RES 1));
    GROUP g36 ((ATOM NAME O12) & ( RES 1));
    GROUP g37 ((ATOM NAME O13) & ( RES 1));
    GROUP g38 ((ATOM NAME O15) & ( RES 1));
    GROUP g39 ((ATOM NAME O16) & ( RES 1));
    GROUP g40 ((ATOM NAME O14) & ( RES 1));
    GROUP g41 ((ATOM NAME O23) & ( RES 1));
    GROUP g42 ((ATOM NAME O24) & ( RES 1));
    GROUP g43 ((ATOM NAME O25) & ( RES 1));
    GROUP g44 ((ATOM NAME O26) & ( RES 1));
 
    GROUP g45 ((ATOM NAME O23) & ( RES 1));
    GROUP g46 ((ATOM NAME O11) & ( RES 1));
    GROUP g47 ((ATOM NAME O12) & ( RES 1));
    GROUP g48 ((ATOM NAME O13) & ( RES 1));
    GROUP g49 ((ATOM NAME O15) & ( RES 1));
    GROUP g50 ((ATOM NAME O16) & ( RES 1));
    GROUP g51 ((ATOM NAME O14) & ( RES 1));
    GROUP g52 ((ATOM NAME O22) & ( RES 1));
    GROUP g53 ((ATOM NAME O24) & ( RES 1));
    GROUP g54 ((ATOM NAME O25) & ( RES 1));
    GROUP g55 ((ATOM NAME O26) & ( RES 1));
 
    GROUP g56 ((ATOM NAME O24) & ( RES 1));
    GROUP g57 ((ATOM NAME O11) & ( RES 1));
    GROUP g58 ((ATOM NAME O12) & ( RES 1));
    GROUP g59 ((ATOM NAME O13) & ( RES 1));
    GROUP g60 ((ATOM NAME O15) & ( RES 1));
    GROUP g61 ((ATOM NAME O16) & ( RES 1));
    GROUP g62 ((ATOM NAME O14) & ( RES 1));
    GROUP g63 ((ATOM NAME O22) & ( RES 1));
    GROUP g64 ((ATOM NAME O23) & ( RES 1));
    GROUP g65 ((ATOM NAME O25) & ( RES 1));
    GROUP g66 ((ATOM NAME O26) & ( RES 1));
 
    GROUP g67 ((ATOM NAME O26) & ( RES 1));
    GROUP g68 ((ATOM NAME O11) & ( RES 1));
    GROUP g69 ((ATOM NAME O12) & ( RES 1));
    GROUP g70 ((ATOM NAME O13) & ( RES 1));
    GROUP g71 ((ATOM NAME O15) & ( RES 1));
    GROUP g72 ((ATOM NAME O16) & ( RES 1));
    GROUP g73 ((ATOM NAME O14) & ( RES 1));
    GROUP g74 ((ATOM NAME O22) & ( RES 1));
    GROUP g75 ((ATOM NAME O23) & ( RES 1));
    GROUP g76 ((ATOM NAME O24) & ( RES 1));
    GROUP g77 ((ATOM NAME O25) & ( RES 1));
 
 
 OUTPUT
 
    HBOND h1 DONOR g1 ACCEPTER g2 DISTANCE 4.0 ANGLE
 60.0 STATS;
    HBOND h2 DONOR g1 ACCEPTER g3 DISTANCE 4.0 ANGLE
 60.0 STATS;
    HBOND h3 DONOR g1 ACCEPTER g4 DISTANCE 4.0 ANGLE
 60.0 STATS;
    HBOND h4 DONOR g1 ACCEPTER g5 DISTANCE 4.0 ANGLE
 60.0 STATS;
    HBOND h5 DONOR g1 ACCEPTER g6 DISTANCE 4.0 ANGLE
 60.0 STATS;
    HBOND h6 DONOR g1 ACCEPTER g7 DISTANCE 4.0 ANGLE
 60.0 STATS;
    HBOND h7 DONOR g1 ACCEPTER g8 DISTANCE 4.0 ANGLE
 60.0 STATS;
    HBOND h8 DONOR g1 ACCEPTER g9 DISTANCE 4.0 ANGLE
 60.0 STATS;
    HBOND h9 DONOR g1 ACCEPTER g10 DISTANCE 4.0 ANGLE
 60.0 STATS;
    HBOND h10 DONOR g1 ACCEPTER g11 DISTANCE 4.0
 ANGLE 60.0 STATS;
 
 
Thank you SIR.

Vijay

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