From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 11 2009 - 14:45:06 CDT

Hi,
  So I looked at the file you sent and it looks to me like it must
have been generated by a charmm build that was compiled with 64-bit
integers, which creates a problem for any non-64-bit code trying to
read them.

There isn't really a clean way for us to support files of this type
on 32-bit machines. My suggestion is to compile your charmm builds
with 32-bit integers when running on 64-bit platforms. The standard
convention for C-based codes on 64-bit platforms is for integers to
be 32-bit quantities, but for longs and pointers to be 64-bit quantities.
It may be that this issue is unique to the PBEQ modules in charmm, but
we should dig into the charmm side of things further to determine what
the best course of action might be on that side.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Mar 09, 2009 at 10:03:30PM +0100, Jure Praznikar wrote:
> I have attached file (pbeq).
>
> XJureX
>
>
> Quoting John Stone <johns_at_ks.uiuc.edu>:
>
> >
> >Hi,
> > If you can send me a gzipped copy of the pbeq file you computed, I may
> >be able to figure out what's going wrong with reading it. I'm guessing
> >that you used a 64-bit charmm build and that charmm is outputting different
> >data when compiled for 64-bit mode than when compiled for 32-bit mode.
> >Any comments you may have about how charmm was compiled would be helpful.
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Sun, Mar 08, 2009 at 05:36:47PM +0100, Jure Praznikar wrote:
> >>I have calculated ele pot(pbeq) using chramm-gui server and I read a
> >>binary chram file in VMD. I have run VMD on my macbook(intel osx10.5).
> >>Everything worked OK.
> >>
> >>Then I made some ele. pot. calculations on our computers(intel-Linux).
> >>After that I tried to read binary file again on my macbook. But VMD
> >>answer to me
> >>with next message(error):
> >>"pbeqplugin) length record != 44, unrecognized format (length: 939524096)
> >>ERROR) Could not read file
> >>/Users/jure/Desktop/dr/pb_results/thym/2fofc/step2_pbeq.phi80"
> >>
> >>What is a problem?
> >>
> >>I have used next VMD and CHARMM versions:
> >>VMD for MACOSXX86, version 1.8.6 (April 6, 2007)
> >>CHARMM - c36a1
> >>
> >>
> >>XJureX
> >>
> >>
> >>
> >>
> >
> >--
> >NIH Resource for Macromolecular Modeling and Bioinformatics
> >Beckman Institute for Advanced Science and Technology
> >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> >
>

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078