Re: mail about autoionize plugin

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Fri Jul 27 2018 - 08:07:33 CDT

Dear Vidhyasankar
,

the error was originated in psfgen when reading your psf file, so before
adding the ions. When you said "run well in dynamics" are you saying that
you ran precisely the pair
 tutmemprot3.psf
​ ​
and
newtutmem2.pdb
files
and the simulation ran successfully?

Best

João

On Thu, Jul 26, 2018 at 8:40 AM Vidhya Sankar <
vidhyasankar7928_at_remove_yahoo.com> wrote:

> Hello Namd users
> when i use the following command to neutralize command
>
> autoionize -psf tutmemprot3.psf -pdb newtutmem2.pdb -neutralize
>
>
> Autoionize) Reading tutmemprot3.psf/newtutmem2.pdb...
> clearing structure, preserving topology and aliases
> reading structure from psf file tutmemprot3.psf
> Error processing angles
>
>
> But my system run well in dynamics without any error should i neutralize
> or not
>
>
> With regards
> S.Vidhyasankar
>
>
>

-- 
……………………………………………………...
João Vieira Ribeiro
Theoretical and Computational Biophysics Group
Beckman Institute, University of Illinois
http://www.ks.uiuc.edu/~jribeiro/
jribeiro_at_ks.uiuc.edu
+1 (217) 3005851

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