Re: [AMBER] Xleap - disappearance of selection when trying to relax selection

From: Scott Brozell <>
Date: Thu, 11 Jun 2020 02:32:57 -0400


On Wed, Jun 10, 2020 at 11:29:07AM -0400, David A Case wrote:
> On Wed, Jun 10, 2020, Billiot, Eugene wrote:
> >I think I have identified where the problem lies. We are using mixed
> >forcefields to describe an amino acid based surfactant (the hydrophobic
> >tail identified by the GAFF forcefield and amino acid polar head groups
> >identified by the protein forcefield). When we ran antechamber on the
> >surfactant and only used the GAFF forcefield to describe the entire
> >surfactant molecule we did not observe the problem. So Now I just need
> >to identify what I did wrong in using the mixed forcefields to describe
> >the amino acid based surfactant.
> Ah...starts to make some sense. The "relax selection" command in xleap
> doesn't actually use the force field that would be used in sander. For
> speed and generality, it uses a very simplified model. Somehow, it
> looks like it getting confused by either the atomic elements or
> something about the bonding with your mixed atom types.
> Try building and relaxing entirely with gaff. That should(?) get you
> structures. Then you can input those structures and generate the mixed
> force fields you want.
> OR: just avoid relaxing the structures: a subsequent minimization in
> sander will do about the same thing. (Not guaranteed though.)
> My *guess* is that literally no one understands the innards of the
> "relax selection" protocol enough to track down its problems in corner
> cases. Would be glad to be proved wrong about this....

Please send the details and files to reproduce; note that you may need
to perform some redundant saves, but you probably have already done
that if you've had to redo things. Note also that tleap has the select,
relax, deselect commands.

This looks straightforward to debug, probably not straightforward to
fix, but straightforward to patch for a more informative and graceful


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Received on Thu Jun 11 2020 - 00:00:03 PDT
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