VMD-L Mailing List

From: Indrajit Deb (biky2004indra_at_gmail.com)
Date: Wed Apr 01 2020 - 21:24:17 CDT

Hello Josh,
Thanks for your response!
Your assumption is absolutely correct. I have checked three of my restraint
files and found that two of them have one empty line at the ends; whereas
the third file (the chirality restraint file) doesn't have that empty line
at the end and I agree with you that it happened due to the early
termination of the chirality plugin.

I have a ternary complex of protein, DNA and RNA. I did some sanity checks
as follows:

   - for protein (multiple chains) only - no early termination of chirality
   plugin
   - for DNA (two chains) only - no early termination of chirality plugin
   - for RNA (one chain) only - no early termination of chirality plugin
   - for protein+DNA - no early termination of chirality plugin
   - for protein+RNA - no early termination of chirality plugin
   - for DNA+RNA - *measure imprp: empty atom index*
   - for protein+DNA+RNA - *measure imprp: empty atom index*

It seems that there is a problem in recognizing when DNA and RNA both are
present. Could you please double check if I am correct? If you want I can
share the pdb file of the ternary complex that I am using.

Thank you
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

On Wed, Apr 1, 2020 at 7:26 PM Josh Vermaas <joshua.vermaas_at_gmail.com>
wrote:

> 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
>>
>