VMD-L Mailing List

From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Fri Sep 07 2007 - 10:50:23 CDT

Does VMD have this capability yet? An extension possibly?

To what extent can VMD be used to build and parameterize a new molecule (a
new ligand for instance, in drug discovery)?

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