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

From: David A Case <>
Date: Wed, 10 Jun 2020 11:29:07 -0400

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....


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Received on Wed Jun 10 2020 - 08:30:02 PDT
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