Re: [AMBER] PB Bomb in pb_aaradi(): No radius assigned for atom

From: Sangita Kachhap <>
Date: Tue, 11 Aug 2015 19:45:08 +0530


I have added inp=1, and radiopt=0 in &gb but it is giving following

InputError: Unknown variable inp in &gb
 Enter ` --help` for help

On 2015-08-11 6:34 pm, Jason Swails wrote:

> On Tue, Aug 11, 2015 at 8:09 AM, Sangita Kachhap <>
> wrote:
>> I have taken default input just to check of AMBER14, following are the inputs. #input file for GB and PB calculation &general startframe=5 endframe=100 interval=5, verbose=2 keep_files=0 / &gb igb=5, saltcon=0.150, / &pb istrng=0.15 fillratio=4.0 /
> ‚ÄčTry setting inp=1 and radiopt=0 in the &pb section. The error you are
> seeing likely results from using "optimized" radii with the inp=2 nonpolar
> solvation free energy model. The more commonly used model for nonpolar
> solvation energies is a simple SASA-based model specified by inp=1.
> HTH,
> Jason

Sangita Kachhap
Senior Research Fellow
C/O Dr. Balvinder Singh
Bioinformatics centre
CSIR-Institute of Microbial Technology
Chandigarh, Sector-39A, INDIA
AMBER mailing list
Received on Tue Aug 11 2015 - 07:30:03 PDT
Custom Search