On Tue, May 22, 2012, anyiphysics.gmail.com wrote:
>
> I'm trying to simulate a protein with an AMP-bound ligand. I went through
> all the steps following the antechamber tutorial and added all the
> parameters to this ligand. However, I found that the structure of my ligand
> changed completely after I saved it as a pdb file using Leap.
You don't say anything about what commands you used, nor how the structure
"completely changed". Generally, one uses antechamber to create a library
file for a ligand (say AMP). This can be stored in one of several formats.
Then, a leap script has two key points: a "loadAmberPrep" (or loadMol2 or
loadOff) command that makes the unit known to LEaP, followed by a loadPdb
command, which brings in the desired coordinates of both the protein and
ligand.
> I heard that
> in antechamber, sqm will optimize (minimize) the structure and change the
> conformation of the ligand. Is it true? How can I maintain the original
> conformation?
The "problem" is the opposite: as far as I know, it is not as easy as it
should be to access the minimized coordinates from sqm run, and to get them
into the output mol2 file. I'm cc-ing this to Junmei in case he feels
inspired...
....dac
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Received on Tue May 22 2012 - 04:00:02 PDT
