[AMBER] tLeap adding non-library hydrogens

From: David Poole <thepoole.ucdavis.edu>
Date: Wed, 4 Jan 2017 11:07:31 +0100

Okay, here is a fun one.

I'm putting together a model in tleap, I have a mol2 file with the
correct structure and a series of PDB files that contain multiple
copies of the 'residue' defined by the mol2 file.

These files either have the crystal hydrogens, no hydrogens, or
hydrogens added by Chimera.

In all three of these cases, extra hydrogens are added, in the case of
'no hydrogens' starting point, there are also numerous missing

I've had tleap also write out the element from the mol2, and it works fine.

The names of the hydrogens added by any method 'should be' the same.

I am not sure what to do, this rather frustrating to say the least. I
am running AmberTools15, so maybe would this have been fixed with any
changes to 16? I will test it today as well.


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Received on Wed Jan 04 2017 - 02:30:03 PST
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