Dear Prof. Case,
After considering of your remind, I separated the ligand into three
fregments, and loaded into xleap, I almost made it. But I found another
problem. Since I add two caps of ACE and NME to the small molecule, but
antechamber didn't treat them as mentioned in tutorial A1, especially the
atom types. However, if I changed it in the output mol2 file of
antechamber, this time was parmchk that could not get some bond and angle
parameters.
Another question, the atom type of the carbon in both ACE and NME is CT,
while it is CX of the carbon in the backbone and CT in some sidechains.I
simply change CT to CX, will that make some difference?
The attached files are for checking, Thanks so much!
On Thu, Nov 10, 2011 at 5:21 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> 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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--
Best Regards,
Qinghua
Ph.D. student
Juelich Research Center
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Received on Fri Nov 11 2011 - 03:30:03 PST
