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

From: James Starlight <>
Date: Wed, 2 Aug 2017 15:56:45 +0200

Thanks again, David!

As I did in Xleap a thousands years ago - to add ACE group, from the N
term, two hydrogens bound to N should be removed and the ACE carbon
atom should be added.

So to add caps in tleap I should to write some script which will
modify the atoms (e.g to remove H1 ang H2 of the first residue to C of
ACE) and the number of residues (starting from 1 ACE) in initial pdb,

Does the capping is necessary assuming that tleap recognizes first
and last residues (and I hope to neutralize making its termi as COOH
and NH2) as N-res and C-res in final topology?


2017-08-02 15:42 GMT+02:00 David A Case <>:
> 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.
> ...dac
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Received on Wed Aug 02 2017 - 07:00:05 PDT
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