[AMBER] MMPBSA (inp=1 or inp=2)??

From: Thakur, Abhishek <axt651.miami.edu>
Date: Fri, 15 Jul 2016 15:53:44 +0000

Hi I am doing MMPBSA calculation

I need some help to figure out that I should use inp=2 or inp=1 in PB.

Moreover some place I can see people using script for PB analysis in

istrng=0.100, prbrad=1.4, radiopt=0, inp=2,
indi=1.0, exdi=80.0, sander_apbs=0, scale=2.0,
cavity_surften=0.0378, cavity_offset=-0.5692

At some place


inp=2, radiopt=0

At manual


So I am unable to find out what are other terms for, moreover I am seeing if I go with manual and does not use inp=1 or 2 then I get an error
PB Bomb in pb_aaradi(): No radius assigned for atom 66 CB 2C

So now I am confused which script to follow, first one or second one, as the script given in manual is giving error.

Moreover among those two script I should use inp =1 or inp=2 that also concerns me.
As I cannot find what is difference between both of them.

Thanking you,
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Received on Fri Jul 15 2016 - 09:00:02 PDT
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