Dear Amber Users,
I’m recently studying membrane proteins (dopamine receptors) and planing on using MMPBSA.py to calculate the binding free energy between the ligand and receptor. I’m quite new to free energy calculation and after reading the tutorial and manual, I’m still a little confused. Can I ask some questions about the parameter settings of the implicit membrane?
The MD was done under explicit conditions (membrane: POPC, water: TIP3P, Ions: NaCl).
1. How can I find out the best position to put the membrane center (mctrdz) and the thickness (mthick)?
2. If the protein is just a receptor rather than ion channels, should I still set poretype = 1?
3. In the sample input file for MMPBSA with membrane proteins in Amber manual, bcopt was set to 10 and eneopt to 1. But under the detailed explanation of eneopt option, it was emphasized that eneopt=1 requires a nonzero CUTNB and BCOPT = 5. What value should I use for bcopt and eneopt respectively?
4. To run this calculation, I prepared 3 parameter/topology files (only complex, protein, ligand) and only kept protein and ligand in the MD trajectory. Is there any other files I need to make? In the MMPBSA tutorial on the website, the solvated parameter/topology file of the complex was also used via -sp option, but when I use it there was an error. Is it necessary to use the -sp option?
5. Here are the parameter settings that I’m planning to use. Can I ask for some suggestion?
&general
use_sander=1,
startframe=1, endframe=100, interval=1,
keep_files=0, debug_printlevel=2
/
&pb
radiopt=0, indi=20.0, istrng=0.150,
fillratio=4, ipb=1, nfocus=1,
bcopt=10, eneopt=1, cutfd=7.0, cutnb=99.0,
npbverb=1, solvopt=2, inp=2,
memopt=1, emem=7.0, mctrdz=0, mthick=40, poretype=1,
maxarcdot=15000
/
Thank you so much!
Best wishes,
Haoxi
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Received on Wed Jun 10 2020 - 12:30:02 PDT
