Dear Professor Case:
Use LEaP to read in the mol2 or off files you create for each ligand
> separately; load the corresponding frcmod files (if any); load a pdb file
> with the protein + both ligands; output a parm7/rst7 combination that has
> everything. Give that to NAMD, paying attention to the instructions here:
>
> http://ambermd.org/namd/namd_amber.html
>
thanks a lot for such a concise, clear guidance. My memory was obstructed
by the long use of xplor (albeit no good excuse). Actually, I had learned
from Professor Dupradeau long ago how to set up the above with LEaP, and in
a more complex case, involving bonding between ligands and the protein,
which I could carry out successfully. I'll try that now with the new
ligands/proteins. As the latter is very large, first with the ligands only,
to check their stability under MD, as their FF was built by analogy.
francesco
On Sun, Sep 20, 2015 at 2:40 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Sun, Sep 20, 2015, Francesco Pietra wrote:
> >
> > My aim is to get the FF for a protein bearing the two ligands. As far as
> I
> > know leap does not read parm7/rst. Also, as far as I know, running
> > parm7/rst with NAMD (which I intend to do, having no recent amber
> version,
> > nor money for that) requires a single parm7/rst.Thanks for suggesting a
> > procedure.
>
> Use LEaP to read in the mol2 or off files you create for each ligand
> separately; load the corresponding frcmod files (if any); load a pdb file
> with the protein + both ligands; output a parm7/rst7 combination that has
> everything. Give that to NAMD, paying attention to the instructions here:
>
> http://ambermd.org/namd/namd_amber.html
>
> ...good luck....dac
>
>
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>
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Received on Sun Sep 20 2015 - 08:00:04 PDT
