Balazs Jojart wrote:
> Dear Users,
> I would like to convert my psf/pdb file generated by VMD (psfgen) to
> amber style format.
> Unfortunately, I obtained the following error:
>
> At line 2690 of file _psfprm.f (unit = 20, file = 'my.psf')
> Fortran runtime error: Bad value during integer read.
> PSF CMAP
>
> 6 !NTITLE
> REMARKS original generated structure x-plor psf file
> REMARKS 2 patches were applied to the molecule.
> REMARKS topology ala_ala_ala_autopsf-temp.top
> REMARKS segment P1 { first NTER; last CTER; auto angles dihedrals }
> REMARKS patch NTER P1:1
> REMARKS patch CTER P1:3
>
> 33 !NATOM
> 1 P1 1 ALA N NH3 -0.300000 14.0070 0
Hi Balazs,
This is failing because you are using an X-PLOR PSF file format;
CHAMBER, at this moment in time, only supports native PSFs and extended
native PSFs, i.e. ones generated directly from charmm.
The error you pasted is triggered because the code is expecting the atom
line to be of format:
fmt01='(I8,1X,A4,1X,I4,1X,A4,1X,A4,1X,I4,1X,2G14.6,I8)' :
1 AAL 1 ALA N 56 -0.300000 14.0070 0
0.00000 -0.301140E-02
when in fact it is getting:
1 P1 1 ALA N NH3 -0.300000 14.0070 0
Note the difference in fields containing 56 and NH2.
Granted this situation here could dealt with more gracefully, but due to
the nature of the line-by-line parsing within chamber, there is no way
of ascertaining if the PSF is of this X-PLOR sub format. Conversely, if
the PSF is of the extended format (
http://www.charmm.org/package/changelogs/c31log.html ), a flag "EXT" is
present in the first line of PSF file and hence the parsing code in
chamber can change its flow to accommodate this.
For you current situation, you might be able to find a converter, or
there might be a flag to tell VMD to write the PSF in the charmm native
format.
I did not really investigated in detail about the X-PLOR file format
when developing CHAMBER; we had a very specific goal in mind. I was
aware of X-PLOR's existence, but I recall being irritated that its
creator choose the same file suffix and similar internal format as
charmm PSF's without any machine friendly method to discriminate it as
being a different variant. Ideally, the creator of X-PLOR should have
added a XPLO flag or something like that.
The addition support for X-PLOR may be quite easy to implement in
CHAMBER, however I am time constrained with other tasks at the moment,
hence patches most welcome.
regards,
--
Mark Williamson, Post Doc
Walker Molecular Dynamics Group
Room 395E
San Diego Supercomputer Center
9500 Gilman Drive
La Jolla, CA 92093-0505
Email: mjw at sdsc.edu
Office: 858-246-0827
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 18 2010 - 15:30:02 PST
