Again these are water molecules. They aren't in your MolSystem (and you
almost certainly don't want them there) so the formatConverter can't match
them to anything in your project.
Unless you know you want the water coords for some esoteric reason you
should ensure that your aria run is set NOT to write them to the output
PDB files. If you must analyse the output of this round of calculations
you could use the structures from the last in vacuo iteration (it8 in the
default setup).
Marie-Laurence Tremblay <[log in to unmask]> wrote:
Hi Brian,
That seemed to have solved my problem with TIPS but now I can't seem to
link the resonances and it seems to be a format error:
Error: no chain mapping found for chain 'WAT1'.
Error: no chain mapping found for chain 'WAT1'.
Error: no chain mapping found for chain 'WAT1'.
Selected naming system PDB has 36% match with atom names.
Error: seqCode 1 not valid for chainCode 'A' - ignoring.
[...]
Error: seqCode 1 not valid for chainCode 'A' - ignoring.
Error: seqCode 2 not valid for chainCode 'A' - ignoring.
Error: seqCode 2 not valid for chainCode 'A' - ignoring.
Error: seqCode 2 not valid for chainCode 'A' - ignoring.
Error: seqCode 2 not valid for chainCode 'A' - ignoring.
I'm using the name format for PDB.
Marie
On Mon, Apr 30, 2012 at 1:49 PM, Brian Smith
<[log in to unmask]>wrote:
> On Mon, 30 Apr 2012, Marie-Laurence Tremblay wrote:
>
> I'm trying to import .pdb files generated by ARIA back into analysis
but
>> I get
>> this message and the .pdbs wont load:
>>
>> "Cannot find file:
>> Cannot find ChemComp XML file other, TIP."
>>
>> I go through Structure>Structures>import to try and import those files.
>>
>
> TIP are the waters for the water refinement I think. You don't usually
> need these - there's a check box in the ARIA GUI to turn off the output
of
> the waters. In general the direct import into analysis won't work for
> non-standard things (other than just proteins or nucleic acids in other
> words).
>
>
> It doesn't work either through the format converter
>> (import>coordinates>PDB). It says that the files can't be read even
though
>> they look fine.
>>
>
> Try importing as pseudopdb
>
> Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac
uk
> Institute of Molecular, Cell and Systems Biology & School of Life
Sciences,
> College of Medical, Veterinary & Life Sciences,
> Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
> Tel: 0141 330 5167/6459/3089 Fax: 0141 330 4600
> ------------------------------**------------------------------**--------
--
> The University of Glasgow, charity number SC004401
--
Marie-Laurence Tremblay, PhD candidate
Department of Biochemistry and Molecular Biology
Dalhousie University
5850 College St.
Halifax NS, Canada
B3H 1X5
[log in to unmask]
Phone:902-494-4812
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