From: Ashar Malik (
Date: Sun Sep 09 2018 - 03:16:05 CDT

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 <>

> 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 <>
> wrote:
>> The measure h-bonds command? Or ask the plugin for detailed output?
>> -Josh
>> On 2018-09-08 02:16:24-06:00 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.