[gmx-users] How to combine Slipid FF with amber FF?
rajatdesikan at gmail.com
Sun Aug 31 14:20:47 CEST 2014
Slipids are already compatible with Amber. Just download the proper
lipid.itp file (DPPC.itp, DMPC.itp, ...) from the Slipids website, and
include the below line in your .top after processing your protein with
pdb2gmx (and selecting some Amber FF).
; Include lipid topology
Of course, you can change the name of the lipid.itp according to the
lipids in your system.
The order in which this appears in your .top matters. If you add the
lipids to your simulation box and then solvate it, the above line must
come prior to the water.itp
On 8/31/14, Yorquant Wang <wangykoo at gmail.com> wrote:
> Hi all,
> I want to do a membrane protein simulation and I want to use amber FF
> for protein (my target protein contains many beta sheet secondary
> structures). But forcefield.ff file in the web:
> http://people.su.se/~jjm/Stockholm_Lipids/Downloads.html, contains only
> lipids parameter. I don't know how to conbined those lipid parameter
> with amber99sb-ildn.ff.
> Is there anybody who can help me? Thank you very much.
> Yukun Wang
> PhD candidate
> Institute of Natural Sciences && College of Life Science, Shanghai Jiao
> Tong University
> Cell phone: 13621806236.
> China Shanghai
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Rajat Desikan (Ph.D Scholar)
Prof. K. Ganapathy Ayappa's Lab (no 13),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore
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