On 11/09/2011 04:22 PM, David A Case wrote:
>> p = loadpdb protein.pdb
>> l = loadpdb ligand.pdb
>> c = combine {p l}
>> [addions, solvateoct, saveamberparams]
>
> I agree that this ought to work as well, although it is far less common as an
> approach. Are the coordinates of p and l in the output incprd file the same
> ones as in protein.pdb and ligand.pdb? If so, this indeed sounds like a bug;
> if you can post a (small) example showing the problem, we can take a look at
> it.
David,
I can't exactly follow you here, because for me the "combine approach"
worked as expected -- without any bugs.
The coordinate systems of protein.pdb and ligand.pdb were equivalent:
the absolute coordinates in protein.pdb and ligand.pdb place protein and
ligand relative to each other in space exactly as desired.
Now, I am assuming that leap does not change the absolute coordinates
when loading coordinates from a PDB file. Therefore, loading protein.pdb
and ligand.pdb one after the other still keeps the absolute coordinates
and, hence, the desired relative positioning between ligand and protein.
I checked the resulting complex object `c` using `edit c`. The relative
positioning was as desired. I did not check the resulting absolute
coordinates in the resulting incprd file.
Why do you consider it a bug if "coordinates of p and l in the output
incprd file [are] the same ones as in protein.pdb and ligand.pdb?"
For me, this is the expected behavior.
Jan-Philip
>
> ...thanks...dac
>
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Received on Wed Nov 09 2011 - 08:00:03 PST
