VMD-L Mailing List

From: Indrajit Deb (biky2004indra_at_gmail.com)
Date: Wed Apr 01 2020 - 15:41:49 CDT

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