On Thu, Nov 10, 2011, Qinghua Liao wrote:
>
> Firstly, I extracted the small molecule by deleting the standard residues,
> and then added NME and ACE on the two sides of the small molecule,
> respectively. Then I get the new small molecule, so I can use antechamber
> and parmchk to get parameters which can be used in xleap.
>
> Next I loaded the new small molecule into xleap, then I edited it which was
> deleting fragments of NME and ACE, and saved it as a lib (off) file using
> saveoff.
>
> At last, I loaded the entire ligand first, and then the lib file of the
> small molecule, the frcmod file.
You "lig.mol2" file still has the Sybyl atom types, which Amber doesn't know
about. You either need to use antechamber to create a mol2 file with gaff
atom types, or load off/lib files that have gaff atom types.
....dac
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Received on Thu Nov 10 2011 - 08:30:06 PST
