 | |||||||||||||||
 |
 |
 |
|
 |
|
 |
|
 |
|
 |
|
 |
|
 |
 |
AMBER Archive (2007)
Subject: AMBER: Problem in running CARNAL
From: Vijay Manickam Achari (vjrajamany_at_yahoo.com)
Date: Thu Dec 06 2007 - 02:44:09 CST
- Next message: Vijay Manickam Achari: "AMBER: Problem in running CARNAL"
- Previous message: rdauria_at_uci.edu: "Re: AMBER: Making movies in VMD"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
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/
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
- Next message: Vijay Manickam Achari: "AMBER: Problem in running CARNAL"
- Previous message: rdauria_at_uci.edu: "Re: AMBER: Making movies in VMD"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]
|
VU Home |
VUMC Home |
People Finder |
University Calendar
webmaster- modified on January 30, 2009 |