VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Sep 07 2007 - 11:36:45 CDT

D'oh, sorry -- I forgot to reply to all. Thanks :)
Peter

L. Michel Espinoza-Fonseca wrote:
> Just forwarding it to the people who inquired about it :)
>
> ---------- Forwarded message ----------
> From: Peter Freddolino <petefred_at_ks.uiuc.edu>
> Date: 07-sep-2007 11:31
> Subject: Re: vmd-l: peptide builder
> To: "L. Michel Espinoza-Fonseca" <mef_at_ddt.biochem.umn.edu>
>
>
> Just as an addendum, yes, molefacture should be able to build peptides
> from a typed in sequence (the Protein Builder is under the Build menu).
> It should also work for small molecule building, and can be used to
> build structures to pass to paratool. Please let me know if you
> encounter problems.
> Best,
> Peter
>
> L. Michel Espinoza-Fonseca wrote:
>
>>> Does VMD have this capability yet? An extension possibly?
>>>
>>>
>> You could try molefacture to do the task (although I haven't try it yet).
>>
>>
>>
>>> To what extent can VMD be used to build and parameterize a new molecule (a
>>> new ligand for instance, in drug discovery)?
>>>
>>>
>>>
>> You can use the paratool plugin for such task. However, even with its
>> aid, the parametrization process can be quite tedious. Here's the
>> link: http://www.ks.uiuc.edu/Research/vmd/plugins/paratool/
>>
>> Good luck! Michel
>>
>>
>>
>>> Thanks,
>>>
>>> Arneh
>>>
>>>
>>>
>>>
>>>
>>>> No, Molden has a function to automatically build a whole peptide given
>>>> the sequence. It is very simple, is not like building other
>>>> structures, which would certainly be tedious.
>>>> Leandro.
>>>>
>>>>
>>>> On 4/22/06, dimka <newyorkdimka_at_gmail.com> wrote:
>>>>
>>>>
>>>>> Molden is great for adding/modifying small chemical groups. Building
>>>>> an 11-residue fragment will be very tedious. I'd use Modeler for
>>>>> rebuilding the fragment.
>>>>>
>>>>> -d
>>>>>
>>>>> On 4/22/06, Leandro Martínez <leandromartinez98_at_gmail.com> wrote:
>>>>>
>>>>>
>>>>>> Molden does that.
>>>>>> Leandro.
>>>>>>
>>>>>>
>>>>>>
>>>>>> -------------------------------------------
>>>>>> Leandro Martinez
>>>>>> Institute of Chemistry
>>>>>> State University of Campinas
>>>>>> http://www.ime.unicamp.br/~martinez/packmol
>>>>>> -------------------------------------------
>>>>>>
>>>>>> On 4/21/06, John Robinson <johnmrobinson_at_mac.com> wrote:
>>>>>>
>>>>>>
>>>>>>> Can anyone recommend free software that enables one build a peptide
>>>>>>> fragment into a pdb structure that has an 11 residue void.
>>>>>>>
>>>>>>> Thanks,
>>>>>>>
>>>>>>> --John
>>>>>>> --------------------------------------------
>>>>>>> John M. Robinson, M.D., Ph.D.
>>>>>>> mailto:johnmrobinson_at_mac.com
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>