Hi Mark.
Thanks! The problem is solved now. But it gave another error:
chemicalSymbolToZ() cannot map symbol: K , to a Z value
NOTE: If the symbol reported above does not appear to be a valid
element then this most likely means your topology file does not
include element information. The code expects MASS lines in
the topology file to have the following format:
MASS 4 HT 1.00800 H ! TIP3P water hydrogen
your file most likely has
MASS 4 HT 1.00800
you should check this before proceeding.
chemicalSymbolToZ() failed to assign a Z value to an element
K is the potassium ion in the system and in the topology file used, it is
clearly stated:
MASS 8 POT 39.09830 K ! Potassium Ion
But i do not know why it cannot map symbol K. Pls assist.
Thanks and regards,
Colvin
On Fri, Feb 25, 2011 at 3:10 AM, Mark Williamson <mjw.mjw.name> wrote:
> colvin wrote:
> > Hi all,
> >
> > I am trying to convert charmm input files generated from CHARMM-GUI to
> amber
> > prmtop and inpcrd.
>
> > <get_atom_parameters> ERROR, topology file ends without finding all atom
> > types,
> > number found: 34 needed ntypes: 55
> > At line 584 of file _psfprm.f
> > Fortran runtime error: Bad value during floating point read
>
> Hi Colvin,
>
> Can you confirm if all the ATTYPE values in your PSF (6th column):
>
> 1 MEMB 1 DPPC N 40 -0.600000 14.0070 0
> 0.00000 -0.301140E-02
>
> the value 40 here, have an associated ATTYPE value in the MASS section
> in your RTF file:
>
> MASS 1 HL 1.008000 H ! polar H (equivalent to protein H)
> ...snip....
> MASS 40 NTL 14.007000 N ! ammonium nitrogen
>
>
> Regards,
>
> Mark
>
>
>
>
>
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Received on Thu Feb 24 2011 - 23:00:03 PST
