Re: AMBER: tleap load pdb file

From: xiaowen <>
Date: Wed, 9 Feb 2005 12:51:44 -0600 (CST)

Hi, David and Ross,
I reinstall amber8 follow each step what I have done before. Every step
repeatedly finished including the tleap cannot load PDB file.

Then, I use the config.h file (which Ross sent to me), the program cannot be
totally compiled and same error message show again.

I change ..SUFFIXES: .f90 to ..SUFFIXES: .f .c .o .f90, and do it again.
same error message pop.

So I guess that config.h file (Ross used and recommanded ) may not match with
Unix system.

Do you think the compilers version okay?

Here are the versions,
% lslpp -h bos.rte (machine installed 1998!)
% lslpp -h xlfcmp (but compilers are newer...)
% lslpp -h vac.C (C)
% lslpp -h vacpp.cmp.C (C++)
% lslpp -h essl.rte.common (DGEMM, etc. math library)

I already try nuc_ter.pdb file, no helps!

thanks for your time!

> make: 1254-005 Ignored error code 2 from last command.
> cd addles; make install
> xlf90 -qfixed -c -g -g -c lesmain.f
> "lesmain.f", line 105.0: 1515-005 (S) Continuation line is not permitted at
> +beginning of program or after INCLUDE, EJECT, .PROCESS statements or comment
> +directive. Line is ignored.
> Something is very wrong with your configuration, since the Makefile is not
> using the rule that should be specified to compile fortran programs (i.e.,
> it is supposed to run the source through cpp to get a file called _lesmain.f,
> and then to compile that.
> Your config.h file should end with the following lines:
> # default rules for Fortran and C compilation:
> ..f.o: $<
> $(FPP) $< > $(FPP_PREFIX)$<
> $(FC) -c $(FFLAGS) -o $. $(FPP_PREFIX)$<
> ..f90.o: $<
> $(FPP) $< > $(FPP_PREFIX)$<
> $(FC) -c $(FFLAGS) -o $. $(FPP_PREFIX)$<
> ..c.o:
> $(CC) -c $(CFLAGS) $(CPPFLAGS) -o $. $<
> If these are missing, something is wrong with config.h. If they are present
> but being ignored, try changing the following line in config.h, from
> ..SUFFIXES: .f90
> to
> ..SUFFIXES: .f .c .o .f90
> It may be that you will need to use GNU make, rather than IBM's make, but
> this seems like a long shot.
> Also, about the "nuc.pdb" file: you need to insert a TER card between the two
> chains of the DNA in the pdb file.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Feb 09 2005 - 19:53:00 PST
Custom Search