[gmx-users] Hbond occupancy
dallas.warren at monash.edu
Mon Oct 8 22:36:35 CEST 2018
>mmousivand93 <mmousivand93 at ut.ac.ir>
>Dear Dr.Dallas warren
>I am going to analysis H-bond and Hbond occupancy using readHBmap,I downloaded and extracted readHBmap.tar.gz but after typing: ./readHBmap.py -hbm hbmap.xpm -hbn hbond.ndx -f md6.gro -o occupancy.xvg -op pairs.dat ,the message "No hydrogen bonds found above the threshold of 10.0 %%" will appear. The pairs.dat and occupancy.xvg files are empty. When I opened the occupancy.xvg by ConTexT ,the following results could be seen:"
>Results for readHBmap.py (Author: Ricardo O. S Soares)
>--> Found 9 valid hydrogen bond pairs with occupancy of more than 10.0%
>--> The hydrogen bond map (hbond.xpm) has 5001 frames
>Pair ID | donor-acceptor | Atom Number | Occupancy (%) | Pair ID
> I would appreciate any suggestions.
Never used that script, so can't help you there. However, before
using the script, does the hbmap.xpm file contain valid data that you
would expect the script to be able to process? i.e. is the input into
the script valid? If so, then might be an issue with the script, so
contact that person that wrote it. They have provided their email
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
When the only tool you own is a hammer, every problem begins to resemble a nail.
On Mon, 8 Oct 2018 at 09:57, Dallas Warren <dallas.warren at monash.edu> wrote:
> What have you already tried? What results did you get?
> First point of call should be http://manual.gromacs.org/documentation/
> In particular http://manual.gromacs.org/documentation/current/user-guide/cmdline.html
> There you can read through all the scripts that come with the software, how to use them, and what data you can extract.
> Web searches, particularly of the emailing list, will provide lots of information too. If after that, still have questions, then post to the emailing list with what you want to do, what you have tried, and what you are having problems with.
> On Sat, 6 Oct. 2018, 10:12 pm mmousivand93, <mmousivand93 at ut.ac.ir> wrote:
>> Dear users
>> I have run molecular dynamic for DNA-ligand complex and I am going to
>> analysis H-bond and Hbond occupancy using GROMACS, I would appreciate
>> any suggestions.
>> Best regard
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