VMD-L Mailing List

From: Brian Radak (brian.radak_at_gmail.com)
Date: Wed Apr 10 2019 - 05:48:10 CDT

This can definitely be scripted with the "measure dihed" command, but the
selection might still be tricky. Selecting atoms by type is easy enough,
but I suspect that inferring the exact connectivity sequence you want (a
dihedral type) is not implemented as is (I might be wrong).

What does your system look like? It might be easier to use atom names if
you are just searching through identical residues or molecules.

HTH,
BKR

On Tue, Apr 9, 2019, 10:23 PM Ashar Malik <asharjm_at_gmail.com> wrote:

> I noticed your question earlier.
>
> However I failed to understand what you meant by certain types of angles.
>
> What you should be looking at is this command
>
> *dihed atom_list [options]*: Returns the dihedral angle defined by four
> atoms. Same input format as the 'measure bond' command.
>
> which is available here:
> https://www.ks.uiuc.edu/Research/vmd/vmd-1.8.6/ug/node124.html
>
> meaning for a given list of 4 atom indices using
>
> measure dihed <list of 4 atoms>
>
> should give you the dihedral.
>
> Can't help more than this - unless you explain better what you mean by:
>
> I mean different indexes for the dihedral atoms, but same types for them.
>>
>
> On Wed, Apr 10, 2019 at 9:08 AM M K <mahyar.karimi20_at_gmail.com> wrote:
>
>> Any code or software can do that?
>>
>> I am able to visually select dihedral angles, but this is tedious to do
>> for all of them (to reach a statistically good piont).
>>
>> On Wed, Apr 10, 2019 at 10:19 AM M K <mahyar.karimi20_at_gmail.com> wrote:
>>
>>> Can someone help me with this question please?
>>>
>>> On Mon, Mar 25, 2019 at 5:17 PM M K <mahyar.karimi20_at_gmail.com> wrote:
>>>
>>>> Hi,
>>>>
>>>> Is it possible to measure all the dihedral angles of a certain type of
>>>> dihedral in one script? By certain type of a dihedral, I mean different
>>>> indexes for the dihedral atoms, but same types for them.
>>>> Thanks
>>>>
>>>>
>
> --
> Best,
> /A
>