VMD-L Mailing List

From: Amit Jaiswal (amitjai20_at_gmail.com)
Date: Wed Oct 01 2014 - 23:12:13 CDT

Dear Ajasja, Dear Lo,

Many thanks for your suggestions. Previously I had tried Discovery Studio
but was unable to build the peptide. I will try in VMD and will let you
know if I was successful. I will try to merge both the peptides and I come
across any problem I will ask you help one more time. Thanks a lot.

With kind regards
Amit Jaiswal

On Wed, Oct 1, 2014 at 5:19 PM, Tim Lo <timlo_at_hku.hk> wrote:

> 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 下午 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> 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. *
>> *~~~~~~~~~~~~~~~~~~~~~~~~**~~~**~*
>>
>
>
> 

-- 
*Yours Sincerely,*
*~~~~~~~~~~~~~~~~~~~~~~~~**~~~*
*Amit Jaiswal,*
*A.T. Road, Tarajan,*
*Jorhat - 785001,*
*Assam.-------------------------------------------*
*Centre for Bioinformatics,Pondicherry Central University,*
*Pondicherry - 605014,*
*Pondicherry.             *
*~~~~~~~~~~~~~~~~~~~~~~~~**~~~**~*