Dear amber users,
I have a ligand, which is a small molecule attached several standard amino
acids on both side. In order to get the prmtop and inpcrd files of the
ligand, I follow the methods from the tutorial:
http://ambermd.org/tutorials/advanced/tutorial1/
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.
But when I checked the parameters of the ligand, there were still some
missing parameters for bonds and angles. Could someone give me some
suggestions? The attached files are the files I used. Any response will be
appreciated!
--
Best Regards,
Qinghua
Ph.D. student
Juelich Research Center
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Received on Thu Nov 10 2011 - 05:30:06 PST
