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

From: James Starlight <jmsstarlight.gmail.com>
Date: Wed, 2 Aug 2017 12:52:14 +0200

Dear amber users!

Here is an example of my script for amber-16 for tleap of membrane receptor

 printf "set default PBradii mbondi2
source leaprc.${param_set}
loadamberparams frcmod.${param_set}
source ./lipids/GAFFlipid.dat
source leaprc.gaff
source leaprc.water.tip3p
loadamberparams ./lipids/GAFFlipid.frcmod
loadoff ./lipids/PPC.lib
protein = loadpdb ${filenamenoextention}_lipids.pdb
addions protein Cl- 0
addions protein K+ 0
setbox protein centers
solvatebox protein TIP3PBOX { 0.0 0.0 ${mem_z} } 1.5
#check protein

Here my questions:

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

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

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

Thanks so much!


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Received on Wed Aug 02 2017 - 04:00:03 PDT
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