segmentation fault core dumped reg.

[shefin121]

Hi @rasbt
I found the Hbind tool interesting and wish to use the tool Hbind. I have used it in 2018. And now I installed the package and im getting the message
"WARNING: unable to open file (null); Bad address (open_mol2)
Segmentation fault (core dumped)"
I tried it with the example files provided.
The command which i tried is shown below.
shefin@DESKTOP-S8S4EEL:/mnt/f/Hbind-master/Hbind-master$ ./bin/hbind -p ./example_files/1KPF.pdb \ -l ./example_files/1KPF_AMP.mol2

HBIND Version: 1.0.0

Documentation: http://psa-lab.github.io/Hbind
Raschka, Wolf, Bemister-Buffington, Kuhn (2018)
Protein Structure and Analysis Lab, MSU (http://kuhnlab.bmb.msu.edu)
Please help. It is for my Ph. D work.

Thank you
Shefin

[rasbt]

I am sorry to hear that it now causes issues. The code wasn't updated since 2017, so I have no idea why it suddenly doesn't work anymore. Maybe your operating system has substantially changed and you need to recompile it?

EDIT: I do see that I changed one of the files 2 years ago (e0f8bee). I think this was due to an issue that others got when running it. It fixed that issue back then. In your case, maybe you need the original version though.

To get the original version, you could either change that file back, or download everything from this snapshot: https://github.com/rasbt/Hbind/tree/949ca065a3fdc41df4cb350af87793e68171cc8c

[shefin121]

Dear Mam Very happy to say that today I executed successfully the Hbind tool as well as Hbindviz. May I know what is a doneptor? is that the atom which can act both as a donor and an acceptor. With Kind Regards Shefin

…

On Sat, Oct 16, 2021 at 7:48 PM Sebastian Raschka ***@***.***> wrote: I am sorry to hear that it now causes issues. The code wasn't updated since 2017, so I have no idea why it suddenly doesn't work anymore. Maybe your operating system has substantially changed and you need to recompile it? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJSNZP5C4BUR2PH6L3TN5VTUHGCRZANCNFSM5F7OWH4Q> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[rasbt]

Glad it works.

May I know what is a doneptor? is that the atom which can act
both as a donor and an acceptor.

Yes, thats correct

[shefin121]

Sir Thank you for the kind response. With Kind Regards Shefin

…

On Wed, Nov 3, 2021 at 6:20 PM Sebastian Raschka ***@***.***> wrote: Glad it works. May I know what is a doneptor? is that the atom which can act both as a donor and an acceptor. Yes, thats correct — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJSNZP6745SVVNGRABKURPDUKE4YZANCNFSM5F7OWH4Q> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[shefin121]

Dear Sir Can you provide more insights on doneptor. Like whether it is good to have doneptors in a protein ligand complex or what is the importance of doneptors. I couldn't find much information regarding this.\ With Kind Regards Shefin Research Scholar India

…

On Wed, Nov 3, 2021 at 6:20 PM Sebastian Raschka ***@***.***> wrote: Glad it works. May I know what is a doneptor? is that the atom which can act both as a donor and an acceptor. Yes, thats correct — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJSNZP6745SVVNGRABKURPDUKE4YZANCNFSM5F7OWH4Q> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[rasbt]

The atoms that can act as both acceptor and donor ("doneptor") are a bit more flexible so they could potentially increase misrecognition, but they are also relatively rare. Here's a passage from our paper regarding this point:

The second most prevalent case paired a hydroxyl group donor with an oxygen acceptor (24%). Other possibilities for native ligand H-bonding were rare, particularly nitrogen atoms acting as H-bond acceptors, whether on the protein or ligand side. The tendency of hydroxyl groups to contribute only one-quarter of all protein–ligand H-bonds despite having two lone pairs and one proton, all of which can form H-bonds, can be rationalized by the resulting reduction in ligand selectivity. A ligand group with either good donor or acceptor geometry could both interact with that hydroxyl group, bringing the risk of misrecognition. This could have been the basis for negative selection during evolution.

[shefin121]

Thank you Sir

…

On Tue, Nov 9, 2021 at 6:03 PM Sebastian Raschka ***@***.***> wrote: The atoms that can act as both acceptor and donor ("doneptor") are a bit more flexible so they could potentially increase misrecognition, but they are also relatively rare. Here's a passage from our paper regarding this point: The second most prevalent case paired a hydroxyl group donor with an oxygen acceptor (24%). Other possibilities for native ligand H-bonding were rare, particularly nitrogen atoms acting as H-bond acceptors, whether on the protein or ligand side. The tendency of hydroxyl groups to contribute only one-quarter of all protein–ligand H-bonds despite having two lone pairs and one proton, all of which can form H-bonds, can be rationalized by the resulting reduction in ligand selectivity. A ligand group with either good donor or acceptor geometry could both interact with that hydroxyl group, bringing the risk of misrecognition. This could have been the basis for negative selection during evolution. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#3 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AJSNZP7BESLZBRW7VKSFG3TULEILLANCNFSM5F7OWH4Q> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.