[gmx-users] How to combine Slipid FF with amber FF?

[Yorquant Wang]

Hi,
   I have done that according to your advice and  when I do the command
grompp, I get such a error:
Fatal error:
Atomtype NTL not found
---------------------
this is my top file:

#include "amber99sb-ildn.ff/forcefield.itp"
#include "POPC.itp"
#include "protein-amber.itp"
#include "amber99sb-ildn.ff/ions.itp"
#include "amber99sb-ildn.ff/tip3p.itp"

[ system ]
; Name
membrane protein
[ molecules ]
; Compound #mols

protein          2
POPC             72
SOL               3337
NA                  18
CL                  22




2014-08-31 20:20 GMT+08:00 rajat desikan <rajatdesikan at gmail.com>:

> Hi,
>
> 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
>
> Regards,
>
>
> 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
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a
> > mail to gmx-users-request at gromacs.org.
> >
>
>
> --
> Rajat Desikan (Ph.D Scholar)
> Prof. K. Ganapathy Ayappa's Lab (no 13),
> Dept. of Chemical Engineering,
> Indian Institute of Science, Bangalore
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>



-- 
Yukun Wang
PhD candidate
Institute of Natural Sciences && College of Life Science, Shanghai Jiao
Tong University
Cell phone: 13621806236.
China Shanghai