AMBER Archive (2003)

Subject: Carnal problem...

From: Andrei Leitão (ierdna_at_yahoo.com)
Date: Thu Feb 06 2003 - 16:17:49 CST

 Hi AMBER users,

 I am trying to get PDB coordinates from mdcrd coordinates
generated by SANDER.
 I found in AMBER Manual (pages 215-216) an example about
that, but some problems messages appeared about the file
format.
 I started with this following file format:
FILES_IN
  STREAM s1 aaa_md_fim.mdcrd;
FILES_OUT
  COORD c1 ke.p PDB;
DECLARE

OUTPUT
  COORD c1 s1 SELECT (1 3);
END

(and this line command: carnal -O -i aaa_analin -o
aaa_analout -p aaa.prmtop &)

 This message error appeared:
input aaa_analin
Reading parm file (aaa.prmtop)
parm: opening aaa.prmtop
> FILES_IN
FILES_IN
........^
Error in aaa_analin line 1: beginning: expected FILES_IN
    Last token was FILES_IN

 After that I changed the analin file to:
FILES_IN STREAM s1 aaa_md_fim.mdcrd;
FILES_OUT COORD c1 ke.p PDB;
DECLARE
OUTPUT COORD c1 s1 SELECT (1 3);
END

 Now the error changed to the end of line one:
> FILES_IN STREAM s1 aaa_md_fim.mdcrd;
Using default parm (aaa.prmtop) for STREAM s1
 (box will be read from stream)
stream: opening aaa_md_fim.mdcrd
FILES_IN STREAM s1 aaa_md_fim.mdcrd;
....................................^
Error in aaa_analin line 1: FILES_IN: unexpected token
    Last token was

 Finally I changed analin to:
FILES_IN STREAM s1 aaa_md_fim.mdcrd
FILES_OUT COORD c1 ke.p PDB
DECLARE
OUTPUT COORD c1 s1 SELECT (1 3)
END

 ... and the error was:
> FILES_OUT COORD c1 ke.p PDB
FILES_OUT COORD c1 ke.p PDB
.........^
Error in aaa_analin line 2: STREAM: expected file name, got
keyword: FILES_OUT
    Last token was FILES_OUT

 I found some questions about CARNAL in the Archive of
AMBER email reflector and FAQ, but no one was related to
the analin format file.

 That you in advance about any hint,

=====
Andrei Leitão
Doutorando em Química Medicinal
Graduante Student in Medicinal Chemistry
NEQUIM - Núcleo de Estudos em Química Medicinal - Brasil
UFMG - Universidade Federal de Minas Gerais
NEQUIM - Medicinal Chemistry Group - Brazil
UFMG - Federal University of Minas Gerais

_______________________________________________________________________
Busca Yahoo!
O serviço de busca mais completo da Internet. O que você pensar o Yahoo! encontra.
http://br.busca.yahoo.com/