Hi
I have taken a psf file from the charmm for ala.psf but when I use chamber I
get the same error as reported earlier. The psf format should be the
original charmm and the command is the one from the tutorial
chamber -top top_all27_prot_na.rtf -param par_all27_prot_na.prm -psf ala.psf
-crd ala.pdb -cmap
PSF
2 !NTITLE
* MBOND/CHARMM TEST : GENERATION OF ALANINE DIPEPTIDE USING UNITED ATOM
FORCEFI
* DATE: 7/31/95 15:47:18 CREATED BY USER:
alper
12 !NATOM
1 DIPE 1 ACE CH3 14 0.000000E+00 15.0350 0
2 DIPE 1 ACE C 11 0.550000 12.0110 0
3 DIPE 1 ACE O 51 -0.550000 15.9994 0
4 DIPE 2 ALA N 38 -0.350000 14.0067 0
5 DIPE 2 ALA H 1 0.250000 1.00800 0
6 DIPE 2 ALA CA 12 0.100000 13.0190 0
7 DIPE 2 ALA CB 14 0.000000E+00 15.0350 0
8 DIPE 2 ALA C 11 0.550000 12.0110 0
9 DIPE 2 ALA O 51 -0.550000 15.9994 0
10 DIPE 3 CBX N 38 -0.350000 14.0067 0
11 DIPE 3 CBX H 1 0.250000 1.00800 0
12 DIPE 3 CBX CA 14 0.100000 15.0350 0
could be something other than the fomat issue?
On Mon, Sep 13, 2010 at 6:01 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Jorgen,
>
> I should add that, as far as I am aware, it should be fairly easy to
> convert
> the psf file. You should just be able to load it into Charmm as an XPLOR
> psf
> and then write the psf back out as a regular psf. Then you should be able
> to
> process it through Chamber.
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: Mark Williamson [mailto:mjw.mjw.name]
> > Sent: Monday, September 13, 2010 8:11 AM
> > To: AMBER Mailing List
> > Subject: Re: [AMBER] chamber At line 2692 of file _psfprm.f
> >
> > On 13/09/2010 16:00, Jorgen Simonsen wrote:
> > > Hi
> >
> > > At line 2692 of file _psfprm.f
> > > Fortran runtime error: Bad value during integer read
> > >
> > > I have generated my psf using VMD so it is a little bit different
> > than
> > > charmm's psf format can chamber handle the psf for NAMD as well? I am
> > using
> > > ambertool 1.4.
> >
> >
> > Hi,
> >
> > You might want to have a look at this thread:
> >
> > http://archive.ambermd.org/201002/0288.html
> >
> > 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.
> >
> > regards,
> >
> > Mark
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Wed Sep 22 2010 - 05:00:04 PDT
