[gmx-users] pdb2gmx generates very large .top for lipids with charmm36-nov2016.ff

[Jonathan Saboury]

So I found out why I didn't use charmm-gui initially, when using the
protein membrane builder it removes the ligand minocycline. I have found a
solution, on the unlikely chance what I have done will help someone, I'm
going to post what I did.

Since I used transformations on the protein (aligning to z axis, moving
along z axis) it made it difficult to align minocycline with the charmm-gui
protein as well as needing to fix hypervalent carbons.

I first aligned the xtal and charmm-gui proteins with uscf chimera. Then
outputted the minocycline coords and fixed the bonds with Spartan '08. Then
I used charmm-gui Ligand Reader & Modeler to output charmm36.itp and
MIY.itp. I renamed charmm36.itp to charmm36_2.itp and added both to the
charmm-gui directory and included them in .top. I combined the two pdbs
(protein/lipids/water and minicycline) and removed any TER/END's in the
middle. I also added minocycline to index.ndx.

Thanks for the help!

- Jonathan




On Mon, Mar 13, 2017 at 9:24 PM, Jonathan Saboury <jsabou1 at gmail.com> wrote:

> I honestly forgot why (took too long, erred, or both) so I tried to do
> charm-gui again. From my current attempt it is taking a while. I'm on the
> last step and I'll keep checking the output.
>
> I'll keep you updated when something happens.
>
> Thanks again, your help is invaluable!
>
> - Jonathan
>
> P.S. I am seriously impressed on all the projects you are on and still
> have time to do user help XD
>
> On Sun, Mar 12, 2017 at 5:59 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 3/12/17 8:36 PM, Jonathan Saboury wrote:
>>
>>> Hello all,
>>>
>>> I generated a 3:1 POPE:POPG bilayer with charmm-gui, ran the
>>> minimization,
>>> equilibration, and production runs given. Then I copied the 10ns
>>> production
>>> run .gro to a different folder so that I can run it with
>>> charmm36-nov2016.ff instead of the ff given.
>>>
>>>
>> Why?  The topology CHARMM-GUI gives you still works, and that's sort of
>> the purpose - it gives you everything you need for the system.
>>
>> When running the command "gmx_mpi pdb2gmx -ff charmm36-nov2016 -f
>>> old_membrane_lipid_only.pdb -o old_membrane_pdb2gmx.pdb -p topol.top
>>> -water
>>> tip3p" it generates a very large .top file (26.8 MB) that has [ atoms ]
>>> and
>>> perhaps other headings.
>>>
>>> I was under the impression that the .top should have been small and just
>>> contained the include line for where the POPE and POPG .itps were in the
>>> charmm36-nov2016. Did I do something wrong? Would this give me a
>>> simulation
>>> that isn't accurate?
>>>
>>>
>> No, because pdb2gmx will generate an explicit copy of the topology for
>> every instance of every residue, which leads to an extremely redundant
>> topology with many copies of lipids and water.  As stated above, there is
>> no need to re-generate your topology.  Use what CHARMM-GUI gives you.  We
>> worked hard to make it easy for the end user :)
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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>