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

From: Sangita Kachhap <sangita.imtech.res.in>
Date: Tue, 11 Aug 2015 19:45:08 +0530

 

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

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

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

> On Tue, Aug 11, 2015 at 8:09 AM, Sangita Kachhap <sangita.imtech.res.in>
> wrote:
>
>> I have taken default input just to check MMPBSA.py 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
----------------------------------------------
 
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Received on Tue Aug 11 2015 - 07:30:03 PDT
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