[gmx-users] Can I use slipids.ff + charmm36.ff to create a system?

[Carlos Navarro]

Hi Mark,
I’ll look in more detail the literature regarding this situation.
Thanks a lot for your reply.
Best,
Carlos

-- 
Carlos Navarro Retamal
Bioinformatic Engineering. PhD
Postdoctoral Researcher in Center for Bioinformatics and Molecular
Simulations
Universidad de Talca
Av. Lircay S/N, Talca, Chile
T: (+56) 712201 <//T: (+56) 712201> 798
E: carlos.navarro87 at gmail.com or cnavarro at utalca.cl

On August 23, 2017 at 10:23:03 AM, Mark Abraham (mark.j.abraham at gmail.com)
wrote:

Hi,

The emails have been arriving, but you're asking a complicated series of
questions. You need to find some literature that shows these protein and
lipid force fields were parameterized in a compatible way, and even then
you may need to show that you in fact get a physically reasonable result.
Only once you've got that sorted does integrating details like the atom
type descriptions into a hybrid forcefield folder become work worth doing.
We haven't written code to make "combine two *.ff folders" work smoothly,
because usually that's a nonsense operation...

Mark

On Wed, Aug 23, 2017 at 3:07 PM Carlos Navarro <carlos.navarro87 at gmail.com>
wrote:

> Dear gmx users,
>
> This is the third time I’m sending this email, but for some reason is not
> been accepted.
>
> I’m trying to set up a system consisting in a protein embebed into a
> bilayer. The whole system contains approximately ~400000 atoms, so to
speed
> up the simulation I'm using virtual sites.
>
> I had no issue by converting my initial structure (protein) into a .gro+vs
> And for the lipid coordinates and parameters I’m using the one published
in
> the following article:
> http://pubs.acs.org/doi/pdfplus/10.1021/acs.jctc.5b01202 files here->
> https://zenodo.org/record/47649#.WZssiHeGMcg (In the link are the
> parameters for POPC, as well as the ffbonded and ffnonbonded for the
slipid
> forcefield).
>
> Unfortunately, since the lipids posses its own forcefield file (located in
> slipids.ff) I don’t how how to include the parameters in the ‘main’
> topology file, because if I do add the slipid forcefield in I get the
> following error:
>
> Fatal error:
>
> Syntax error - File forcefield.itp, line 5
>
> Last line read:
>
> '1 2 yes 0.5000 0.8333'
>
> Found a second defaults directive.
>
> error, which make sense.
> But also If I tried to add only the .itp file of POPCvs to the .top file
> gromacs complain about the atomtypes:
>
> ERROR 1 [file POPCvs.itp, line 66]:
>
> Atomtype MCH3N not found
>
>
> If I’m not mistaken, I have read some articles were people indeed can
> combine different forcefield, but sadly I don’t know how to do that.
> If this is imposible to do, does someone know vsite parameters for POPC
> that can be use in charmm36?
> Hope someone can help me.
> Best regards,
> Carlos
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