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From: Sasthi Charan Mandal (sasthi.phys_at_gmail.com)
Date: Sun Mar 17 2019 - 03:58:09 CDT

---------- Forwarded message ---------
From: Sasthi Charan Mandal <sasthi.phys_at_gmail.com>
Date: Sun, Mar 17, 2019 at 2:27 PM
Subject: Re: vmd-l: hydrogen bond calculations
To: Roshan Shrestha <roshanpra_at_gmail.com>

Thank you. The cut off is 3.4 A and angle = 20 degree.
Can you please comment on occupancy?

On Sun, Mar 17, 2019 at 1:12 PM Roshan Shrestha <roshanpra_at_gmail.com> wrote:

> Hi,
> What were the cut off distance and angle used in both VMD and
> Discovery Studio?
> Thanks
>
> On Sun, 17 Mar 2019, 13:17 Sasthi Charan Mandal, <sasthi.phys_at_gmail.com>
> wrote:
>
>> Dear VMD users,
>> I have calculated hydrogen bonds between protein and DNA in protein-DNA
>> complex using Discovery Studio and also using vmd. In vmd I can not find
>> atoms which participate in h-bonding, just the residues are there. And the
>> other thing is for single pdb vmd gives less hbonds compared to Discovery
>> Studio, this is one doubt and the another thing is how much percentage of
>> occupancy should I count for h-bond when many pdb's there. Kindly someone
>> help me.
>> sincerely
>> Sasthi
>>
>