AMBER Archive (2003)

Subject: AMBER: STREAM problems : segmentation fault with CARNAL

From: Jean-François Taly (jftaly_at_jouy.inra.fr)
Date: Wed Oct 15 2003 - 05:03:35 CDT

Dear AMBER community,

 I'm using carnal of the 6.0 package of AMBER.

I am trying to do Hbonds study of my protein trajectories cut in several
crd files by using restart files.
I have no problem when i use only one of the crd files.
The problem is a segmentation fault when i put several crd files in the
carnal.in.

Has anyone experienced this problem before?
 Does anyone no what might happen?
Thanks a lot for help

Best regards,
jean-françois

******here the in file :

FILES_IN
PARM p1 ../../../FP/ABFP_mod_H_wat.parm;

STREAM s1 p1
a1.traj
a2.traj;

FILES_OUT
  HBOND hb1 carnalHBOND_SS_ABFP_4.0_60.0 LIST;
  HBOND hb2 carnalHBOND_SW_ABFP_4.0_60.0 LIST;
  HBOND hb3 carnalHBOND_WS_ABFP_4.0_60.0 LIST;

DECLARE
 GROUP grp1 s1 (SOLUTE);
 GROUP grp2 s1 (RES NAME WAT);

OUTPUT
  HBOND hb1 DONOR grp1 ACCEPTOR grp1 DISTANCE 4.0 ANGLE 60.0 STATS;
  HBOND hb2 DONOR grp1 ACCEPTOR grp2 DISTANCE 4.0 ANGLE 60.0 STATS;
  HBOND hb3 DONOR grp2 ACCEPTOR grp1 DISTANCE 4.0 ANGLE 60.0 STATS;
END

****** out file :

                         - CARNAL -
                          AMBER 6.0
 
                      COORDINATE ANALYSIS
 
 
input carnalHBONDABFP.in
> FILES_IN
> PARM p1 ../../../FP/ABFP_mod_H_wat.parm;
Reading parm file (../../../FP/ABFP_mod_H_wat.parm)
parm: opening ../../../FP/ABFP_mod_H_wat.parm
../../../FP/ABFP_mod_H_wat.parm title:
                                                                                

>
> STREAM s1 p1
> a1.traj
 (box will be read from stream)
> a2.traj;
stream: opening a2.traj
Segmentation fault

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