On Tue, Apr 19, 2016, peter.schmidtke.discngine.servier.com wrote:
>
> In natural residues yes. But sometimes I have small molecules where the
> atom name is not unique (as output of tleap). Like for instance for
> ATP. This is actually the problem.
This is illegal, and tleap should be warning you about this. It will use the
first atom of a given name, and ignore the rest (which accommodates "alternate
conformers" that are often present in PDB files.) It's not clear how you
created the ATP libraries (and I don't need to know this), but you should
avoid this situation--as Dan pointed out, all kinds of programs, including
cpptraj, assume that atom names are unique within residues.
...regards...dac
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Received on Tue Apr 19 2016 - 11:30:04 PDT
