AMBER Archive (2002)

Subject: problems on IBM AIX

From: Giovanni Fossati (gfossati_at_rice.edu)
Date: Thu Sep 12 2002 - 20:43:52 CDT

                                              Thursday September 12, 2002
Dear users and developers,
I have a few problems to submit to your attention.

1* amber6/sander_classic :
   When I try to run it, with the same script that works on linux, I get this
   error message:

> 1525-090 The NAMELIST READ statement cannot be completed because an
> incorrect character was encountered in a NAMELIST group name or item
> name. The program will recover by discontinuing further processing of
> the READ statement.

   I have seen that a few months ago somebody else (Vlad Cojocaru) asked
   for a clue about this same error message, but I was not able to find an
   answer/solution to it in the archive.

   Does anybody have a hint?

   b) there is another "oddity" in the behavior of the program.
      Even though it would not be supposed to, it also opens the mdvel file.
      I guess that it is because it is using some default input parameters
      because it can not read my namelist, but still I am puzzled by the fact
      that sander seems to "die" immediately without running a MD... so how
      can it be opening files?
      I say that it dies immediately because it instantaneously moves to
      the next run (I am running it inside a loop, to have many short MDs).

2* amber7:
   When compiling ptraj is stops with this error:

> Building on: IBM,7040-681 under AIX
> cc -c -Drs6000 -DNMLEQ -DCLINK_PLAIN -DMEM_ALLOC -DMASSLIB ptraj.c
> "ptraj.c", line 4385.37: 1506-045 (S) Undeclared identifier transformCheckOverlap.
> make: 1254-004 The error code from the last command is 1.

   I see that transformCheckOverlap is defined in actions.c.
   But there is no linking yet in the above command, right? (-c switch is on).
   So, how can the poor ptraj.c resolve this.
   It actually complains that is "undeclared" rather than "unresolved"...
   and so it sounds like there might be a problem with include files.
   Has anybody encountered this problem before?

3* amber6:
   compiling trajectory.c in ptraj
   Error message:

> Building on: IBM,7040-681 under AIX
> cc -c -Dibm_aix -DISTAR2 -DMASS -DREGNML -DNMLEQ -DMEM_ALLOC -DEWALD -DCLINK_PLAIN trajectory.c
> "trajectory.c", line 271.21: 1506-275 (S) Unexpected text 'int' encountered.
> "trajectory.c", line 1446.13: 1506-019 (S) Expecting an array or a pointer to object type.
> "trajectory.c", line 1446.21: 1506-019 (S) Expecting an array or a pointer to object type.
> "trajectory.c", line 1446.29: 1506-019 (S) Expecting an array or a pointer to object type.
> "trajectory.c", line 1698.17: 1506-275 (S) Unexpected text 'double' encountered.
> "trajectory.c", line 1698.28: 1506-275 (S) Unexpected text 'double' encountered.
> "trajectory.c", line 1982.17: 1506-275 (S) Unexpected text 'double' encountered.
> "trajectory.c", line 1982.28: 1506-275 (S) Unexpected text 'double' encountered.
> make: 1254-004 The error code from the last command is 1.

   ???
   I am not a big C user, but the calls at those lines look fine to me.
   This is the one at 1982.

      dumpCharmmTrajectory(fpout, traj, atoms, x, y, z, box, set)
           FILE *fpout;
           charmmTrajectoryInfo *traj;
           int atoms;
 --> double *x, double *y, double *z;
           double *box;
           int set;
      # endif

I really wish some of you can shed light on these problems...
Thank you very very much.
Have a great day,

        Giovanni Fossati

------------------------------------------------------------------------------
 Dr. Giovanni Fossati +---------------------------+
 Dept. of Physics and Astronomy, MS 108 | Ph : (713)-348-3425 |
 Rice University | Fax : (713)-348-5143 |
 6100 Main street, Houston, TX 77005, USA | e-mail: gfossati_at_rice.edu |
-------------------------------------------------+---------------------------+