Hi Anna,
I haven't tried this myself, but the error message probably tells you
exactly what the issue is and how to solve it.
When I look in toph19.inp for example, the MASS lines don't have the
element as the 5th string (whereas for example top_all22_prot.inp does have
this).
Try to simply modify toph19_eef1.inp: add the element of the atom type as
the 5th string on the MASS lines.
Hope this helps,
Marc
On 30 July 2012 22:36, Anna Tarakanova <annat.mit.edu> wrote:
> I am trying to create AMBER prmtop and inpcrd files from CHARMM
> param19_eef1 and toph19_eef1 parameter and topology files. I am using
> CHAMBER, with the following command:
>
> chamber -cmap \
> -top toph19_eef1.inp \
> -param param19_eef1.inp \
> -psf input.psf \
> -crd input.pdb \
> -p output.prmtop \
> -inpcrd output.inpcrd \
>
> I get the following error however:
>
> chemicalSymbolToZ() cannot map symbol: ! , 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
>
> It seems the format of the topology file is not compatible. Is it possible
> to create AMBER parameter and coordinate files with CHARMM implicit solvent
> force fields?
>
> Thanks,
>
> Anna
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 31 2012 - 01:00:04 PDT
