VMD-L Mailing List

From: Tim Lo (timlo_at_hku.hk)
Date: Wed Oct 01 2014 - 06:49:33 CDT

Hi Richard,

I am not very familiar with other programs but in my opinion, using the
script template in the topotools website given by Ajasja is convenient
enough. In the script, you just need to state the psf and pdb files of
the two molecules and your desired psf and pdb file names of the merged
molecule. That's it! These pieces of information are in principle
necessary, even if there is a program to merge molecules in the GUI. I
don't think the merging procedure can be reduced to anything simpler.

Do you have any recommendations to simplify the merging procedure?

Regards,
Tim
Research Assistant
The University of Hong Kong

On 2014/10/1 ?? 06:54, Richard Wood wrote:
> Couldn't one do this easier in another program?
>
> Richard
>
> ------------------------------------------------------------------------
> *From:* owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of
> Ajasja Ljubetič [ajasja.ljubetic_at_gmail.com]
> *Sent:* Wednesday, October 01, 2014 4:45 AM
> *To:* Amit Jaiswal
> *Cc:* vmd-l_at_ks.uiuc.edu
> *Subject:* Re: vmd-l: Reg: Peptide dimer
>
> I'm sure it's possible. What have you tried so far?
> If I would have to do it, I would load the peptide twice (into two
> molecules), orient the second molecule, merge them using topotools
> <https://sites.google.com/site/akohlmey/software/topotools/topotools---documentation#TOC-mergemols-list-of-molecule-ids-> and
> save them to a pdb.
>
> Good luck,
> Ajasja
>
> On 1 October 2014 10:42, Amit Jaiswal <amitjai20_at_gmail.com
> <mailto:amitjai20_at_gmail.com>> wrote:
>
> Hi Everyone,
>
> I would like to know if is it possible to prepare peptide dimer in
> VMD. If yes, how and if no what are the possible ways to prepare
> it? Please let me know and thanks in advance.
>
>
> With kind regards,
> Amit Jaiswal
>
> --
>
> *Yours Sincerely,*
> *
> *
> *~~~~~~~~~~~~~~~~~~~~~~~~**~~~*
> *Amit Jaiswal,
> *
> *A.T. Road, Tarajan,
> *
> *Jorhat - 785001,
> *
> *Assam.
> -------------------------------------------
> *
> *Centre for Bioinformatics,
> Pondicherry Central University,*
> *Pondicherry - 605014,
> *
> *Pondicherry.
> *
> *~~~~~~~~~~~~~~~~~~~~~~~~**~~~**~*
>
>