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

[Jonathan Saboury]

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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