VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon Mar 09 2009 - 11:57:21 CDT

On Mon, 2009-03-09 at 09:45 -0500, John Stone wrote:

john,

i'm switching mailer programs and hit the wrong hotkey when
replying to the OP (and not including the list).

we had a charmm developer in our group for a while, so i know
that charmm on linux is compiled with gfortran and that uses
by default 64-bit record seperators in fortran unformatted,
and not 32-bit ones like everybody else (well, there is a flag
to set it, but next to nobody uses it).

it doesn't look like the pbeqplugin has support for that,
so basically copying the "black magic" from dcdplugin should
do the trick (or most of it).

cheers,
   axel.
> 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
> >
> >
> >
> >
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.