VMD-L Mailing List

From: Sasthi Charan Mandal (sasthi.phys_at_gmail.com)
Date: Sun Sep 09 2018 - 08:44:18 CDT

Thank Mr. Ashar, I'll check it out.

On Sun, Sep 9, 2018 at 1:46 PM Ashar Malik <asharjm_at_gmail.com> wrote:

> Read this for command line
>
> If using GUI -- there are checkboxes that need checking and paths that
> need to be assigned --- if in windows make sure you have access to write
> where you are saving data by default and then go check that location.
>
> On Sun, Sep 9, 2018 at 4:04 PM Sasthi Charan Mandal <sasthi.phys_at_gmail.com>
> wrote:
>
>> Dear Josh,
>> Thank you for the answer. But can you please tell me how do I get
>> the detailed output?
>> Sasthi
>>
>> On Sunday, September 9, 2018, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
>> wrote:
>>
>>> The measure h-bonds command? Or ask the plugin for detailed output?
>>>
>>> -Josh
>>>
>>>
>>> On 2018-09-08 02:16:24-06:00 owner-vmd-l_at_ks.uiuc.edu wrote:
>>>
>>> Dear all,
>>> I want to calculate the hydrogen bonds between protein and dna
>>> atomwise in vmd. So I used vmd for this calculation but vmd gives the
>>> hydrogen bonding in residue wise for an example residue-132-side with
>>> dna-11-side. But vmd does not give the hydrogen bond between atoms i.e.
>>> which atom in protein making hydrogen bond with which dna atom. So if you
>>> give any suggestion of how to calculate hydrogen bonds atomwise, it would
>>> be very much helpful.Thanks in advance.
>>>
>>>
>
> --
> Best,
> /A
>