Hi
I was going through manual for
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
/
found that all the things set up are default parameters.
So If things are default then do I need to write it on my script?
So If I use this script
istrng=0.100,
inp=2, radiopt=0
/
It should be same? Because in upper script everything is set as default value? It should take it automatically if I don't mention it in my script right?
I was also seeing that cavity_surften=0.0378 only works in inp=1.
Now I am confused I should go with inp=1 or 2.
If anyone can explain me
inp = Non polar optimization method (Default=2)
Which gives better result?
As I was seeing that non polar model for PB is more destablized than simple model.
Does it mean if I use inp = 1 then it will use simple model?
________________________________
From: Thakur, Abhishek <axt651.miami.edu>
Sent: Friday, July 15, 2016 4:53:44 AM
To: amber.ambermd.org
Subject: [AMBER] MMPBSA (inp=1 or inp=2)??
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
istrng=0.100,
inp=2, radiopt=0
/
At manual
istrng=0.100,
/
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,
-AT
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=CwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=XOaVbwdRkzS099jspY_eFjj0EYz5PdXozwOG5qaWCv4&s=oMD_0p00LvvNDglMFo4gqnhkgXtEogu-X7jk2VKlCxQ&e=
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jul 15 2016 - 09:30:02 PDT
