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

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 11 Aug 2015 11:44:55 -0400

On Tue, Aug 11, 2015 at 11:08 AM, Sangita Kachhap <sangita.imtech.res.in>
wrote:

>
>
> Sorry for that. Now I have added inp=1, and radiopt=0 in &pb, run has
> completed but giving following warning.
>

​These are informational -- it's simply telling you that the inp=2 defaults
for the surface tension was changed to the default appropriate for the
inp=1 model.

HTH,
Jason



>
> Warning: inp=1 was old default
> Warning: cavity_surften=0.0378 not recommended for inp=1, switching to
> inp=1 default value: 0.0050
> Warning: cavity_offset=-0.5692 not recommended for inp=1, switching to
> inp=1 default value: 0.000
> Warning: sprob=.557 not recommended for inp=1, switching to inp=1
> default value: 1.400
> Warning: inp=1 was old default
> Warning: cavity_surften=0.0378 not recommended for inp=1, switching to
> inp=1 default value: 0.0050
> Warning: cavity_offset=-0.5692 not recommended for inp=1, switching to
> inp=1 default value: 0.000
> Warning: sprob=.557 not recommended for inp=1, switching to inp=1
> default value: 1.400
> Warning: inp=1 was old default
> Warning: cavity_surften=0.0378 not recommended for inp=1, switching to
> inp=1 default value: 0.0050
> Warning: cavity_offset=-0.5692 not recommended for inp=1, switching to
> inp=1 default value: 0.000
> Warning: sprob=.557 not recommended for inp=1, switching to inp=1
> default value: 1.400
>
> On 2015-08-11 8:13 pm, Jason Swails wrote:
>
> > On Tue, Aug 11, 2015 at 10:15 AM, Sangita Kachhap <sangita.imtech.res.in
> >
> > wrote:
> >
> >> I have added inp=1, and radiopt=0 in &gb but it is giving following
> error.
> >
> > ​I said &pb, not &gb.
> >
> > 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
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Aug 11 2015 - 09:00:03 PDT
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