VMD-L Mailing List

From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Wed Apr 01 2020 - 18:26:44 CDT

Hi Indrajit,

NAMD, for whatever reason, expects an empty line at the end of every file
it reads in (that's why you are getting an ABNORMAL EOF). Yours likely
doesn't have one because the chirality plugin terminated early after having
one of its assumptions violated. Without knowing more about the structure,
I can't know why specifically you had this issue. What is in your system?
Is it just proteins and nucleic acids, which the plugin should handle
pretty well?

-Josh

On Wed, Apr 1, 2020 at 3:27 PM Indrajit Deb <biky2004indra_at_gmail.com> wrote:

> Hi,
> I am using VMD for the input file preparation for MDFF calculations in
> NAMD. When I was preparing the chirality restraint file in VMD Tk-console,
> I found the following error message:
>
> >Main< (inputs_test) 24 % chirality restrain -o
> step1_pdbreader-chirality.txt
> WARNING: Ignoring residue(s) with missing atoms...
> measure imprp: empty atom index
>
> I continued preparing the input files. After that when I am using the NAMD
> input file to run the calculations in NAMD, it is giving the following
> error when it is reading the chirality restrain file:
>
> Info: READING EXTRA BONDS FILE step1_pdbreader-extrabonds.txt
>
> Info: READING EXTRA BONDS FILE step1_pdbreader-cispeptide.txt
>
> Info: READING EXTRA BONDS FILE step1_pdbreader-chirality.txt
>
> FATAL ERROR: ABNORMAL EOF FOUND - buffer=*improper 52275 52272 52298 52277
> 50 37.11127090*
>
>
> ------------- Processor 0 Exiting: Called CmiAbort ------------
>
> Reason: FATAL ERROR: ABNORMAL EOF FOUND - buffer=*improper 52275 52272
> 52298 52277 50 37.11127090*
>
>
>
> [0] Stack Traceback:
>
> [0:0] [0x143cd3e]
>
> [0:1] [0x4fa66d]
>
>
>
> Can anyone please help me to solve the problem?
>
> Thanks
> Indrajit
>
> --------------------------------------------------------------------------------------------------------------
> Indrajit Deb
> Postdoctoral Researcher
> *https://sites.lsa.umich.edu/frank-lab/
> <https://sites.lsa.umich.edu/frank-lab/>*
> Department of Biophysics (Room - 3004)
> University of Michigan
> 930 N University Avenue
> Ann Arbor, Michigan - 48109, USA
> Alternate emails: indrajitdeb81_at_gmail.com, idbmbg_s_at_caluniv.ac.in,
> ideb_at_umich.edu
> Mobile: +17343588364
>