Hi all,
I am sending the email again, pls assist.
I am having problem converting charmm input files generated from CHARMM-GUI
to amber prmtop and inpcrd.
The command used:
chamber -cmap -top top_all_22prot36lipid.rtf -param
par_all_22prot36lipid.prm -psf step5_assembly.psf -crd step5_assembly.crd -p
chamber.prmtop -inpcrd chamber.inpcrd
and the 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 2:48 PM, colvin <colvin4367.gmail.com> wrote:
> 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
>>
>>
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Mon Feb 28 2011 - 01:00:03 PST
