[gmx-users] How to build and simulate POPE/POPG bilayer with gromos54a7 force field

[paul buscemi]

You might try the ATB website

http://atb.uq.edu.au/molecule.py?molid=368385#panel-md

you can  create the lipid and submit your pdb ,but most likely it already exists in their data base. Use the  modified Gromos54a7 ff and the pdb and  itp provided by ATB.. 

Good luck !

Paul


> On Nov 4, 2019, at 8:05 AM, daniel depope <nevjernik at gmail.com> wrote:
> 
> I want to simulate POPE/POPG bilayer with gromos54a7 ff (expanded with
> lipids parts, as explained in Lemkul's kalp tutorial).
> 
> 1. I tried CHARMM-gui website - I got bilayer in step 5, but can't finalize
> because there are no gromos ff option. So I looked for pope and popg
> gromos54a7 topology, but with no succes so I stacked. Any suggestions how
> to proceed?
> 
> 2.  Another option was to build that bilayer with packmol, but I can't find
> a way to do so (I know how to build homogenuos bilayer).
> 
> 3. POPE molecule from CHARMM-gui website have 125 atoms. I have some old
> POPE molecule with only 52 atoms. Last one has only two hydrogen atoms. Can
> anyone explain why is that a case.
> 
> Obvioiusly I missed some basics, I apologize for that, but I need
> clarification to move on..
> 
> Thanks
> -- 
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