On 11/09/2011 04:38 PM, Jan-Philip Gehrcke wrote:
> 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.
Correction: expected behavior for me is that the relative positions of
objects loaded consecutively from different input files are kept. Of
course, when saving the entire system coordinates to an inpcrd file, the
coordinate center can be changed (is leap doing that?).
>
> Jan-Philip
>
>
>>
>> ...thanks...dac
>>
>> _______________________________________________
>> 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 Wed Nov 09 2011 - 08:00:04 PST
