AMBER Archive (2004)

Subject: AMBER: carnal

From: Julien Pecher (julien.pecher_at_u-picardie.fr)
Date: Mon Feb 16 2004 - 07:17:33 CST

Dear all,

It is my input (for carnal) to measure the gyration radius during the molecular
dynamics

FILES_IN
PARM p1 ../prmtop;
STREAM s1 ../md5.mdcrd.gz ../md6.mdcrd.gz ../md7.mdcrd.gz ../md8.mdcrd.gz;
STREAM s2 ../md9.mdcrd.gz ../md10.mdcrd.gz ../md11.mdcrd.gz ../md12.mdcrd.gz;
STREAM s3 ../md13.mdcrd.gz;
FILES_OUT
TABLE tab1 radgyr.tbl;
DECLARE
GROUP gall (RES 1-21);
OUTPUT
TABLE tab1 gall%radgyr;
END

 I do not arrive has to obtain my output (of all my dynamics) in entirety

My question is as follows :

what I have a problem on the level of my input?
so yes which is this problem?

my output file

                          - CARNAL -
                          AMBER 6.0

                      COORDINATE ANALYSIS

input stdin
>
> FILES_IN
> PARM p1 ../prmtop;
Reading parm file (../prmtop)
parm: opening ../prmtop
> STREAM s1 ../md5.mdcrd.gz ../md6.mdcrd.gz ../md7.mdcrd.gz ../md8.mdcrd.gz;
Using default parm (../prmtop) for STREAM s1
stream: opening ../md6.mdcrd.gz
stream: opening ../md7.mdcrd.gz
stream: opening ../md8.mdcrd.gz
stream: opening ../md5.mdcrd.gz
> STREAM s2 ../md9.mdcrd.gz ../md10.mdcrd.gz ../md11.mdcrd.gz ../md12.mdcrd.gz;
Using default parm (../prmtop) for STREAM s2
stream: opening ../md10.mdcrd.gz
stream: opening ../md11.mdcrd.gz
stream: opening ../md12.mdcrd.gz
stream: opening ../md9.mdcrd.gz
> STREAM s3 ../md13.mdcrd.gz;
Using default parm (../prmtop) for STREAM s3
stream: opening ../md13.mdcrd.gz
> FILES_OUT
> TABLE tab1 radgyr.tbl;
> DECLARE
> GROUP gall (RES 1-21);
Using default stream
** Group gall: 316 atoms
> OUTPUT
> TABLE tab1 gall%radgyr;
> END
(EOF reached on ../md5.mdcrd.gz)
stream: opening ../md6.mdcrd.gz
(EOF reached on ../md9.mdcrd.gz)
stream: opening ../md10.mdcrd.gz
(EOF reached on ../md13.mdcrd.gz)
STREAM s3: no more files/crds (iteration 50000)
SUMMARY

    thanks for advance

Julien Pecher
Laboratoire de Biophysique |Tel: +33 (0)3 2282-7498
Faculte de Pharmacie, 1 rue des Louvels |Fax: +33 (0)3 2282-7469
80037 Amiens Cedex 1, France |email:
julien.pecher_at_u-picardie.fr

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