Re: [AMBER] Running MMPBSA on protein membrane system built using CHARMMGUI

From: David A Case <>
Date: Sat, 13 Mar 2021 17:08:06 -0500

On Sat, Mar 13, 2021, Chuck is Busy wrote:
>Do you have any better insight on how I can define the 1-4 EEL and 1-4 VDW
>scale factors so I can run PBSA calculations on my protein system? The
>protein membrane system was built in CHARMM-GUI and the CHARMM force field
>but simulated using AMBER.

If you ran the simulation with Amber, you have prmtop files with the
appropriate values of SCEE and SCNB in them (as highlighted here from your

>| Note: 1-4 EEL scale factors are being read from the topology file.
>| Note: 1-4 VDW scale factors are being read from the topology file.

>If I set my radii to mbondi with and set scnb and scee to 1. I
>can get MMPBSA to run this way using sander, but after doing my
>subtractions I get extremely positive values like 1200 to 1700. Wondering
>if there is a more appropriate way to do this..

Why are you changing scnb and scee with parmed? Setting the radii makes
sense to me, but I'm not sure why you want to change scnb and scee.

...hoping the others on the list will correct any mistakes above.


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Received on Sat Mar 13 2021 - 14:30:03 PST
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