Hi James,
Cgenff won't work - that's the Charmm General Force Field and isn't
compatible with the lipid14 and ff99sb force fields. You need to use the
GAFF force field for your ligand.
I would suggest using:
LIPID14
FF12SB
GAFF
Start by making sure you can:
1) Build a pure lipid and get this working using the conversion script.
2) Make sure you can build your ligand correctly using antechamber and
GAFF.
3) Make sure you can build your protein correctly using FF12SB.
4) Make sure you can build your protein ligand complex correctly combining
FF12SB with GAFF.
5) Build your lipid+protein+ligand complex and convert this with the
conversion script.
6) Adjust any namings for the protein and ligand as needed and then build
the entire thing.
Good luck,
All the best
Ross
On 5/7/14, 11:50 PM, "James Starlight" <jmsstarlight.gmail.com> wrote:
>Thanks Jason,
>
>If I understood you correctly there is charmmlipid2amber script which is
>useful for the conversion of pdb made by charm-gui including full complex
>consisted of protein embedded in the solvated bi-layer, isn't it? So
>during
>preparaton of such system having converted pdb I only should provide for
>tleap lipid14 (for lipids), amber99sb (protein) and Cgenff (for ligand)
>params, shouldn't it?
>
>James
>
>
>2014-05-06 15:57 GMT+04:00 Jason Swails <jason.swails.gmail.com>:
>
>> On Tue, 2014-05-06 at 14:15 +0400, James Starlight wrote:
>> > Dear Amber Users!
>> >
>> >
>> > I'm looking for the tutorial with step-by-step workflow of the
>> construction
>> > of membrane-protein system having pre-equilibrated bilayer and
>>protein in
>> > separate pdb's.
>> > Also I'll be thankful if you provide me with some online service wich
>> could
>> > do such taks automaticly (like charm-gui membrane builed for
>>instance).
>>
>> Why not just use CHARMM GUI membrane builder? Or the one in VMD? In
>> fact, the Amber lipid tutorial (shown below) suggests the CHARMM-GUI
>> builder. There's a script "charmmlipid2amber.x" (soon to be updated
>> with a more extensive "charmmlipid2amber.py") script that will convert
>> all of the CHARMM lipid residues into corresponding Amber residues.
>> Then you can use that PDB file with lipid14 and ff14SB to parametrize
>> your system.
>>
>> As for the tutorial, see
>>
>>
>>http://ambermd.org/tutorials/advanced/tutorial16/An_Amber_Lipid_Force_Fie
>>ld_Tutorial.html
>>
>> There's nothing I know of that shows how to insert a membrane-bound
>> protein, but the hard part would be setup. Presumably the CHARMM GUI
>> lipid builder allows you to build such a system, then all you have to do
>> is load the appropriate protein force field (and possibly make sure atom
>> names match).
>>
>> Good luck,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
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>>
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Received on Thu May 08 2014 - 00:30:03 PDT
