VMD-L Mailing List
From: PRITI ROY (priitii.roy_at_gmail.com)
Date: Sun Feb 12 2017 - 13:10:36 CST
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,
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%
On Sun, Feb 5, 2017 at 7:00 AM, Chitrak Gupta <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?
> On Sat, Feb 4, 2017 at 1:12 AM, PRITI ROY <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.
>> On Fri, Feb 3, 2017 at 10:15 PM, Chitrak Gupta <chgupta_at_mix.wvu.edu>
>>> 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,
>>> On Fri, Feb 3, 2017 at 12:58 AM, PRITI ROY <priitii.roy_at_gmail.com>
>>>> 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.
>>>> Priti Roy