From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Sun May 24 2015 - 08:27:46 CDT
Hi Kevin,
ffTK or paramchem is overkill for this application, since lipids are
modular, and all the atomtypes you need to describe the chemistry
already exist within the lipid forcefield. What you need to do instead
is merge together the topologies for a DOPC lipid with a POPI lipid so
that a PI headgroup is sitting on top of two unsaturated tails. Read up
on how topology files are constructed first, and from there it should be
pretty obvious what needs to be changed to make POPI into DOPI (just one
tail if I remember my lipid nomenclature).
For part 2 of your question, believe it or not, people did membrane
simulations before CHARMM-gui too. :D What I would do is use CHARMM-gui,
and then regenerate the membrane using psfgen after you have renamed a
dummy lipid you used in CHARMM-gui (I recommend DOPC so the lipid tail
double bonds are isomerized correctly) into DOPI.
-Josh
On 5/23/15 1:58 PM, Kevin C Chan wrote:
> Dear Users,
>
> 1) I'm currently trying to do simulations of a membrane containing
> DOPI lipid. There are other types of lipids and I could find all
> of them on CHARM-GUI except DOPI. The closest lipid I could find is
> POPI which only differs from DOPI with one tail. I'm thinking to
> prepare force field for DOPI using ffTK or paraChem. Does anyone have
> experience on this and could share some comments, i.e. which is a
> better tool or what should I prepare as an input?
>
> 2) Also, I'm thinking, even if I obtain the force field for DOPI, how
> could I construct the membrane without CHARM-GUI?
>
> Any answer is highly appreciated.
>
> Thanks in advance,
> Kevin
> City University of Hong Kong
>
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