Hello:

I am having a problem with the PBEQ module. It writes the incorrect format for the commands

! write phi
open write file unit 40 name @pdb.phi80
write PHI kcal unit 40
close unit 40

only when charmm is compiled with the em64t option. I used the intel compiler. This happens for both c34b2 and for c35b2.

When I used the gnu option the format was fine. The gnu option provides correct format for both x86_64 and x86 Linux operating systems.

What do I mean by incorrect format? The resulting @pdb.phi80 file is unreadable by VMD, and the file is about twice as large for the em64t case.

I wish I could quantify this problem better, and there is probably an easy answer to this ( It is not IOFOrmat NOEXtended placed in the PBEQ module.). I used the simple example given in a MMTSB tutorial. The phi80 file is easily read by VMD for a gnu-compiled version of charmm but not for a em64t-compiled version. Try it, and you will see.

Thanks for your help with this.

Regards,

Angelo

When you say "gnu option" I assume that you did not specify x86_64.

On a 64-bit system (em64t) integer variables are 64-bit by default, and some of the information written by WRITE PHI is stored in integer variables. The correct solution is probably to make these 32-bit integers before the unformatted write operation in routine SAVGD1 in source/manip/pbeq*.src.

Hello:

YES. This is correct. For the gnu option, I did not specify x84_64.

Regards,

Angelo

In pbeq2.src, routine SAVGD1, try changing this

INTEGER I
IF(UNIT.GT.0)THEN
IF(PRNLEV.GE.2) WRITE(OUTU,'(3x,A)')
$ 'FIRST RECORD IS: NCLX,NCLY,NCLZ,DCEL,XBCEN,YBCEN,ZBCEN'
IF(PRNLEV.GE.2) WRITE(OUTU,'(3x,A)')
$ ' EPSW,EPSP,CONC,TMEMB,ZMEMB,EPSM'
WRITE(UNIT) NCLX,NCLY,NCLZ,DCEL,XBCEN,YBCEN,ZBCEN

to

INTEGER I
INTEGER*4 NCLX4,NCLY4,NCLZ4
IF(UNIT.GT.0)THEN
NCLX4=NCLX
NCLY4=NCLY
NCLZ4=NCLZ
IF(PRNLEV.GE.2) WRITE(OUTU,'(3x,A)')
$ 'FIRST RECORD IS: NCLX,NCLY,NCLZ,DCEL,XBCEN,YBCEN,ZBCEN'
IF(PRNLEV.GE.2) WRITE(OUTU,'(3x,A)')
$ ' EPSW,EPSP,CONC,TMEMB,ZMEMB,EPSM'
WRITE(UNIT) NCLX4,NCLY4,NCLZ4,DCEL,XBCEN,YBCEN,ZBCEN

Dear Professor Nilsson:

Hooray!!!! That did it! I should have thought of this myself.

Thank you so much.

As a postscript:

When I compiled charmm orginally, I used the keepf and keepo options leaving pbeq2.f in the build/em64t directory:

1. made your suggested changes to pbeq2.f and re-compiled.

2. copied the new pbeq2.o file to the lib/em64t directory.

3. executed the command: ar -vr misc.a pbeq2.o to replace the old pbeq2.o object file with the new one.

4. executed a "make" command in the build/em64t directory

5. copied the resulting charmm.exe executable to exec/em64t/charmm

Thanks again. This is great.

Warm regards,

Angelo

Very good!
The simple standard way is to do the edits to pbeq2.src and then just issue the "install.com em64t" command again.