From: Indrajit Deb (biky2004indra_at_gmail.com)
Date: Wed Apr 01 2020 - 11:15:57 CDT
Hi,
I am using VMD for the input file preparation for MDFF calculations in
NAMD. When I was preparing the chirality restraint file 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?
--------------------------------------------------------------------------------------------------------------
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
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