On Wed, Nov 09, 2011, 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.
OK...this is probably my fault, although both you and Senthil Natesan
are writing on the same thread, and maybe I got things mixed up. But I
suspect that I am not the only person that is now confused.
If you are happy with the "combine approach" and everything works as expected
without any bugs, that is great. If you have other questions/problems, please
start a new thread on the mailing list (that is, don't use the "reply"
command, but compose a new mail with a new subject.)
The problem I *thought* was occuring was that solvateOct seemed not to be
working correctly when the "combine approach" was used. For this problem,
I ask that the following ptraj actions be taken:
input the prmtop and inpcrd files you have
center the protein + ligand
image familiar the water residues
use trajout to save a new restart file
Then look at that restart file: is the protein+ligand now in the center of the
box?
....dac
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Received on Wed Nov 09 2011 - 14:00:03 PST
