Thanks Robert,
I'll give it a go - I suppose I'll have to tell ARIA to use this PDB and
PSF file, but I've been doing that anyway. I had hoped that Analysis would
have a way to add ions directly since it's not that uncommon, but I don't
expect the workaround will be that hard to pull off.
Cheers,
Andrew
--
Dr. Andrew Fowler | University of Iowa
Associate Director | B291 Carver Biomedical Research
Building
Medical NMR Facility | Iowa City, IA 52242
319-384-2937 (office) | 319-335-7273 (fax)
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On 5/19/11 7:03 AM, "Robert Dagil" <[log in to unmask]> wrote:
>Hey Andrew
>
>I too am calculating protein structures with calcium ions in it with
>Aria2, and I can give you the hints you need. It is possible to use Aria2
>for these calculations. Do the following:
>
>* First, of all you need to create a pdb and psf file with the calcium
>added. You can use the generate.inp on the cns-webserver to do this.
>
>* Secondly, you have to make a restraint list (unambig.tbl) with the
>restraints between your backbone and side chain atoms to the calcium
>(named so that it is the same as in the pdb/psf file).
>
>* Finally, you need to make topology definition file and a parameter
>definition file containing information about the protein and the calcium
>for the Aria2 calculations. You can do this by merging the ion.top and
>ion.para from cns with the standard topology and paramater files from the
>aria2 folder.
>
>
>Then you should be up-and-running
>
>
>Best regards
>
>
>Robert Dagil
>Ph.d. studerende
>
>Københavns Universitet
>Biologisk Institut
>SBiNLab
>Ole Maaløes Vej 5
>DK-2200 København N
>
>TLF 35 32 20 79
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