[gmx-users] How to combine Slipid FF with amber FF?
wangykoo at gmail.com
Sun Aug 31 14:42:53 CEST 2014
I have done that according to your advice and when I do the command
grompp, I get such a error:
Atomtype NTL not found
this is my top file:
[ system ]
[ molecules ]
; Compound #mols
2014-08-31 20:20 GMT+08:00 rajat desikan <rajatdesikan at gmail.com>:
> 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
> #include "./DMPC.itp"
> 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
> > 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
> > --
> > Gromacs Users mailing list
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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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