I'm no expert on this step, so I ask someone in the list to correct me
if I'm wrong.
I believe when you load the Mol2 file LEaP will use it only as a
"template" to built the force field terms and add missing atoms. If
you then load a PDB containing your system (enzyme + cofactor), LEaP
will automatically add missing atoms according to the template, but
will get structure from the PDB file. Assuming it recognizes the
molecule as the one described by the Mol2 file, it will add the
correct parameters as well. (Anyone?)
Good luck,
Gustavo Seabra
Professor Adjunto
Departamento de Química Fundamental
Universidade Federal de Pernambuco
Fone: +55-81-2126-7417
On Tue, Jul 19, 2011 at 11:31 AM, David Cantu <cantudav.amber.gmail.com> wrote:
> Thanks,
>
> Yes this is what I meant. In antechamber, sqm will optimize (minimize) the
> structure and change the conformation. This gives me a mol2 and from that
> the frcmod file.
>
> If I want to use the original pdb coordinates as my starting point, do I
> load the mol2? How in XLeap do I load original pdb coordinates, but keep
> mol2 and frcmod parameters?
>
> David
>
> On Tue, Jul 19, 2011 at 5:58 AM, Gustavo Seabra <gustavo.seabra.gmail.com>wrote:
>
>> If you are talking about the minimization of the ligand in antechamber, you
>> *should* expect it to change conformation, basically because its in a
>> different environment than it had in the complex. However, the parameters
>> generated by antechamber are just as valid. You can load those parameters,
>> but use the PDB coordinates for the ligand.
>>
>> Gustavo.
>> --
>> Sent from my iPad.
>>
>> On 19/07/2011, at 01:54, David Cantu <cantudav.amber.gmail.com> wrote:
>>
>> > Dear Amber Users and Developers:
>> >
>> > I have a general question about placing a ligand (or cofactor) in the
>> > correct position and conformation inside an enzyme's active site.
>> >
>> > Suppose you have a ligand (LIG) crystallized in an enzyme. You take LIG's
>> > coordinates, add hydrgens, run it throough antechamber, make the mol2 and
>> > frcmod files. But during minimizations its conformation was changed.
>> >
>> > What I want to do is keep the crystallized conformation of LIG (not the
>> > minimized in the mol2), plus hydrogens. What needs to be done in Leap to
>> > load LIG in its crystallized conformation, but use the parameters derived
>> > from antechamber for GAFF?
>> >
>> > Thank you,
>> >
>> > David
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Received on Tue Jul 19 2011 - 09:00:02 PDT
