Re: [AMBER] Tleap processing of membrane protein in amber-16

From: David A Case <>
Date: Wed, 2 Aug 2017 09:42:27 -0400

On Wed, Aug 02, 2017, James Starlight wrote:

> addions protein Cl- 0
> addions protein K+ 0

Still better in the long run to use CL and K (not Cl- and K+).

> 1) does the addions protein K+ 0 correct meaning that I would like to
> add K+ instead of Na+ for neitralization?

Yes--of course, this will only have an effect if your system originally is
negatively charged.

> 2) which strings should be added to cap N term residue with ACE and C
> term with some another non-charged group like CT2?

You need to edit the input PDB files to have the required end groups. If the
end groups are not standard ones (already in the Amber library), you will
have to create residue libraries for them.

> 3) does the "set default PBradii mbondi2" correct for membrane protein system?

It should be irrelevant, assuming that you would not be using implicit solvent
models here.


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Received on Wed Aug 02 2017 - 07:00:04 PDT
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