Dear amber users,
Last time I asked how to prepare the topology and coordinate files for a
ligand which one small molecule is in the middle and three amino acids are
on the two sides, respectively. Finally I did it, but problems came. I
saved pdb and mol2 files for checking after saving the topology and
coordinate files of the ligand. I found that the amino acids were not
bonded to the small molecule in the pdb file while bonded in the mol2 file
in Chimera, however they were bonded in pymol. At that time I thought they
were bonded. When I checked in VMD after getting a trajectory, I found
they were not bonded. So right now I am not sure they were bonded or not
though I am sure they were bonded in xleap.
So how should I do to make a confirmation on it? Any suggestion will be
appreciated much!
--
Best Regards,
Qinghua
Ph.D. student
Juelich Research Center
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Received on Fri Nov 18 2011 - 06:00:04 PST
