AMBER Archive (2005)

Subject: Re: AMBER: tleap load pdb file

From: xiaowen (xwfang_at_iastate.edu)
Date: Wed Feb 09 2005 - 12:51:44 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 4.3.2.0 (machine installed 1998!)
% lslpp -h xlfcmp 7.1.1.1 (but compilers are newer...)
% lslpp -h vac.C 5.0.1.0 (C)
% lslpp -h vacpp.cmp.C 5.0.0.0 (C++)
% lslpp -h essl.rte.common 3.1.1.0 (DGEMM, etc. math library)

I already try nuc_ter.pdb file, no helps!

thanks for your time!
best!
xiaowen

> 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.

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