AMBER: Problem in running CARNAL

From: Vijay Manickam Achari <vjrajamany.yahoo.com>
Date: Thu, 6 Dec 2007 08:44:09 +0000 (GMT)

Dear experts, I am using CARNAL to analysis intramolecular hydrogen bonding in my bilayer system. 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; HBOND h11 DONOR g12 ACCEPTER g13 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h12 DONOR g12 ACCEPTER g14 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h13 DONOR g12 ACCEPTER g15 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h14 DONOR g12 ACCEPTER g16 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h15 DONOR g12 ACCEPTER g17 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h16 DONOR g12 ACCEPTER g18 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h17 DONOR g12 ACCEPTER g19 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h18 DONOR g12 ACCEPTER g20 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h19 DONOR g12 ACCEPTER g21 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h20 DONOR g12 ACCEPTER g22 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h21 DONOR g23 ACCEPTER g24 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h22 DONOR g23 ACCEPTER g25 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h23 DONOR g23 ACCEPTER g26 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h24 DONOR g23 ACCEPTER g27 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h25 DONOR g23 ACCEPTER g28 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h26 DONOR g23 ACCEPTER g29 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h27 DONOR g23 ACCEPTER g30 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h28 DONOR g23 ACCEPTER g31 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h29 DONOR g23 ACCEPTER g32 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h30 DONOR g23 ACCEPTER g33 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h31 DONOR g34 ACCEPTER g35 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h32 DONOR g34 ACCEPTER g36 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h33 DONOR g34 ACCEPTER g37 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h34 DONOR g34 ACCEPTER g38 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h35 DONOR g34 ACCEPTER g39 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h36 DONOR g34 ACCEPTER g40 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h37 DONOR g34 ACCEPTER g41 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h38 DONOR g34 ACCEPTER g42 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h39 DONOR g34 ACCEPTER g43 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h40 DONOR g34 ACCEPTER g44 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h41 DONOR g45 ACCEPTER g46 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h42 DONOR g45 ACCEPTER g47 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h43 DONOR g45 ACCEPTER g48 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h44 DONOR g45 ACCEPTER g49 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h45 DONOR g45 ACCEPTER g50 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h46 DONOR g45 ACCEPTER g51 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h47 DONOR g45 ACCEPTER g52 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h48 DONOR g45 ACCEPTER g53 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h49 DONOR g45 ACCEPTER g54 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h50 DONOR g45 ACCEPTER g55 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h51 DONOR g56 ACCEPTER g57 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h52 DONOR g56 ACCEPTER g58 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h53 DONOR g56 ACCEPTER g59 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h54 DONOR g56 ACCEPTER g60 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h55 DONOR g56 ACCEPTER g61 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h56 DONOR g56 ACCEPTER g62 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h57 DONOR g56 ACCEPTER g63 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h58 DONOR g56 ACCEPTER g64 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h59 DONOR g56 ACCEPTER g65 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h60 DONOR g56 ACCEPTER g66 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h61 DONOR g67 ACCEPTER g68 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h62 DONOR g67 ACCEPTER g69 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h63 DONOR g67 ACCEPTER g70 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h64 DONOR g67 ACCEPTER g71 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h65 DONOR g67 ACCEPTER g72 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h66 DONOR g67 ACCEPTER g73 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h67 DONOR g67 ACCEPTER g74 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h68 DONOR g67 ACCEPTER g75 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h69 DONOR g67 ACCEPTER g76 DISTANCE 4.0 ANGLE 60.0 STATS; HBOND h70 DONOR g67 ACCEPTER g77 DISTANCE 4.0 ANGLE 60.0 STATS; END and the out put *.log file is as below: - CARNAL - AMBER 6.0 COORDINATE ANALYSIS input stdin > FILES_IN > PARM p1 betaM_lyo.top; Reading parm file (betaM_lyo.top) parm: opening betaM_lyo.top > STREAM s1 betaM_lyo_md02_0100.mdcrd.gz; Using default parm (betaM_lyo.top) for STREAM s1 (box will be read from stream) stream: opening betaM_lyo_md02_0100.mdcrd.gz > > FILES_OUT > HBOND h1 xhb TABLE LIST; > HBOND h2 xhb TABLE LIST; HBOND: file xhb.tab already exists I don't understand why it is not completing the whole calculation? Please help me to Thank you. Vijay ___________________________________________________________ Yahoo! Answers - Got a question? Someone out there knows the answer. Try it now. http://uk.answers.yahoo.com/
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Received on Sun Dec 09 2007 - 06:07:23 PST
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