VMD-L Mailing List

From: Josh (vermaasj_at_msu.edu)
Date: Thu Aug 31 2023 - 09:15:35 CDT

I made a script once to rotate a bond, so I think you could adapt it to
shorten it
(https://urldefense.com/v3/__https://gitlab.msu.edu/vermaaslab/structuremechanic/-/blob/main/structuremechanic.tcl__;!!DZ3fjg!6Zbw_MUuz6mYCDsHz2utS7hFvlokQEVMLf7gezcMQHEbN66mK25835q6KEyzoFTL6rFSope2UlNlb-xZQrI$ ).
The tricky thing about general organic molecules, is if an interior bond
is long, you need to move a whole bunch of atoms. For bond rotation, I
had a scheme set up to select the smaller side so I could perturb as
little as possible. Have you also looked at the new version of
molefacture? It wouldn't surprise me if that functionality was now included.

-Josh

On 8/31/23 5:16 AM, maxim todoru wrote:
> Dear Pr. Sarkar,
> No no, the situation isn't like that, i'm not looking for simulation,
> the whole matter is i perform a topological analysis of an organic
> molecule, and the results i get is like what i explained before (some
> bonds are much longer than the normal), i need to adjusted for nicer
> visualisation, and i think VMD is the only program i know can help me
> (instead of Gaussview).
>
> Le jeudi 31 août 2023, Daipayan Sarkar <sdaipayan_at_gmail.com> a écrit :
>
> Hi,
>
> Are you sure the molecule is built correctly? Said differently,
> this could easily be due to your psfgen script where I assume you
> have topology files for the molecule you are working with. For
> that more specific information about the molecule would be
> necessary. This is of course if you are planning to simulate the
> molecule.
>
> “i need the reduce their length to a specific value”  - I
> personally do not recommend, even if you are using VMD only for
> visualization purposes.
>
> -Daipayan
>
> *From: *"owner-vmd-l_at_ks.uiuc.edu" <owner-vmd-l_at_ks.uiuc.edu> on
> behalf of maxim todoru <mtodoru_at_gmail.com>
> *Date: *Thursday, August 31, 2023 at 3:35 AM
> *To: *"vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
> *Subject: *vmd-l: How to shortening bonds length in a molecule ?
>
> Hi VMD community,
>
> I used VMD to perform the visualisation of some organic molecules,
> but it appears that some bonds length are little tall from normal,
> and i need the reduce their length to a specific value. I failed
> to figure out a solution, and i need some help.
> 

-- 
Josh Vermaas
vermaasj_at_msu.edu
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io