VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jun 05 2015 - 08:29:59 CDT

On Fri, Jun 5, 2015 at 3:47 AM, SaeeD PourasaD <saeedpourasad_at_gmail.com> wrote:
> Dear Axel ,
> Thanks for your kind help .
> I have attached file with this Email.
> I think I just need to change H and O names in this file . right ?

this is a completely superfluous question.

> Best ,
> Saeed.
>
> On Fri, Jun 5, 2015 at 4:04 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> On Fri, Jun 5, 2015 at 2:04 AM, SaeeD PourasaD <saeedpourasad_at_gmail.com>
>> wrote:
>> > Dear VMD users ,
>> >
>> > I Have a XYZ trajectory file and I want to analyse breaking / forming
>> > hydrogen bonds with using of VMD .
>> >
>> > I tried to use h.bonds plugin of vmd but unfortunately I couldn't !
>>
>> that is not very helpful description.
>>
>> > Can you please let me know what I have to do ?
>>
>> the hydrogen bonds plugin is effectively a GUI wrapper around the
>> measure hbonds command in VMD
>> http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.2/ug/node138.html
>> thus it is subject to the same limitations and requirements, e.g. your
>> input has to conform to the naming conventions expected by VMD
>> (typically CHARMM based)
>>
>> most likely your file doesn't conform to the expectations of VMD, so
>> it cannot identify potential H-bond donors and acceptors and possibly
>> not even the hydrogens itself.
>>
>> > I have attached my file with this Email.
>>
>> no, you didn't.
>>
>> > Best ,
>> > Saeed.
>> >
>>
>>
>>
>> --
>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>> International Centre for Theoretical Physics, Trieste. Italy.
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.