VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Sun Feb 12 2017 - 22:13:45 CST

200% occupancy means there are 2 hydrogen bonds between the residue pair at all times. Are the interactions between 2 different proteins in the same simulation system? That is totally doable with the h-bonds plugin (just use two selections, one for one protein and one for another). What is not possible is to get h-bonds between two different simulation systems (which are called molecules by VMD).
Josh Vermaas

Director’s Postdoctoral Fellow
National Renewable Energy Laboratory
joshua.vermaas_at_nrel.gov<mailto:joshua.vermaas_at_nrel.gov>

On Feb 12, 2017, at 12:10 PM, PRITI ROY <priitii.roy_at_gmail.com<mailto:priitii.roy_at_gmail.com>> wrote:

Hii,
At first thanks to Chitrak for your help. Now i understand that H-bond plugin only count h-bond in the given structure. There is any process to get details interacting h-bond of two different protein?

I have another question that the data i got from h-bond plugin there is one column about occupancy. Most of the bond's occupancy 100% but very few have 200% occupancy. What does it means about 200% occupancy?

Some portions of the data,
donor acceptor occupancy
SegAP1-SER270-Main SegAP1-PRO267-Main 100.00%
SegAP1-LYS265-Main SegAP1-VAL350-Main 100.00%
SegAP1-GLN263-Main SegAP1-ILE242-Main 100.00%
SegAP1-HSD253-Main SegAP1-TRP232-Main 100.00%
SegAP1-GLY249-Main SegAP1-ILE243-Main 100.00%
SegAP1-LEU247-Main SegAP1-PRO244-Main 200.00%
SegAP1-ILE242-Main SegAP1-ASN255-Main 100.00%
SegAP1-ASP240-Main SegAP1-GLU237-Main 100.00%

From,
Priti Roy

On Sun, Feb 5, 2017 at 7:00 AM, Chitrak Gupta <chgupta_at_mix.wvu.edu<mailto:chgupta_at_mix.wvu.edu>> wrote:
Hi Priti,

Make sure you are clicking "reply all", so the email chain could be archived for future user (you also stand a better chance of getting help that way).

Make sure you read and understand the documentation of Hbonds plugin (and pretty much anything else that you use). Selection 1 and selection 2 are explained in the documentation. The "molecule" is the molecule that you have loaded, usually you don't have to mess with that unless you have multiple molecules loaded. What error are you getting?

Best,
Chitrak.

On Sat, Feb 4, 2017 at 1:12 AM, PRITI ROY <priitii.roy_at_gmail.com<mailto:priitii.roy_at_gmail.com>> wrote:
Hi Chitrak,
This is working. Thank you so much for your help. I also want to see H-bond between two different interacting protein. What to select in "molecule" option in HBond plugin, this option can't be blank and whats about 2 "selection". I tried this for two different protein but all time showing error. I done this thing in different software but how it can be possible in vmd i don't know.

Thanks again and also in advance. Sorry if any inconveniences is happen.

From,
Priti

On Fri, Feb 3, 2017 at 10:15 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu<mailto:chgupta_at_mix.wvu.edu>> wrote:
Hi Priti,

The hbonds plugin allows you to define a "selection 1" and "selection 2". You could select the two monomers as selections 1 and 2 respectively. If you want the detailed information, make sure you select the "All hbonds" in the "Calculate detailed info for:" option, and check the "Write output files?" option.

Hope this helps,
Chitrak.

On Fri, Feb 3, 2017 at 12:58 AM, PRITI ROY <priitii.roy_at_gmail.com<mailto:priitii.roy_at_gmail.com>> wrote:

Dear all,
I am a beginner in this field. I want to know the only interacting h-bond between the dimer of protein. I used H-bond plugin but it shows all bonding. I wanted to know the interacting backbone-backbone, backbone-sidechain, sidechain-sidechain h-bond between the dimer.

Thanks,
Priti Roy