VMD-L Mailing List

From: Josh Vermaas (joshua.vermaas_at_gmail.com)
Date: Mon Apr 06 2020 - 12:04:07 CDT

Weird. Can you send along the pdb? I'm curious enough to see what's up, but
if you send it to the whole list, somebody else will likely figure it out
faster.
-Josh

On Wed, Apr 1, 2020 at 8:24 PM Indrajit Deb <biky2004indra_at_gmail.com> wrote:

> 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
>>>
>>