VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Fri Sep 07 2007 - 11:35:39 CDT

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
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>