[gmx-users] Protein-Ligand in bilayer

[RAHUL SURESH]

Can anyone explain the right procedure to be followed while building
protein-ligand-popc bilayer?

On Sat, Aug 11, 2018 at 6:48 AM RAHUL SURESH <drrahulsuresh at gmail.com>
wrote:

> Hi Dr. Mark.
>
> The docked complex ( docked using auto dock ) when given as input in
> charmm-gui, it ask for either mol2 file or top and prm file generated using
> paramchem.
>
> But then it shows some atom number mismatch and couldn’t proceed further.
>
> The docked ligand ( pdbqt ) is converted  to pdb format ( by adding
> hydrogen ) using open babel.
>
> Thank you
>
> On Sat, 11 Aug 2018 at 5:01 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> Does CHARMM-GUI not provide a output coordinate file that matches the
>> generated topology file? I don't know why you find its change of ordering
>> a
>> problem.
>>
>> Mark
>>
>> On Thu, Aug 9, 2018, 18:48 RAHUL SURESH <drrahulsuresh at gmail.com> wrote:
>>
>> > Hi users.
>> >
>> > It look so complicated to carry out a protein ligand simulation in Lipid
>> > bilayer system using charmm ff. I have a ligand with 27 atoms ( includes
>> > Hydrogen ). The initial structure (monomer)  is simulated in popc
>> > constructed using charmm gui web page. To construct the same for the
>> > portein-ligand complex is too tedious and very problematic.
>> > The protein-ligand complex is constructed using auto dock from the mol2
>> > file download from Zinc database. The complex structure then is
>> uploaded to
>> > charmm gui and the atom number varies with the mol2 file and pdb file. I
>> > find no way to change the atom order or numbering.
>> >
>> > I feel I m taking a wrong way in these type of simulations. What can be
>> the
>> > better way to do such simulations?
>> >
>> > --
>> > *Regards,*
>> > *Rahul *
>> > --
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> --
> *Regards,*
> *Rahul *
>


-- 
*Regards,*
*Rahul *