[gmx-users] [Fwd: Re: Grompp problems upon embedding a receptor into POPC]

[David van der Spoel]

On Thu, 2003-11-06 at 12:47, David van der Spoel wrote:

> I tried running pdb2gmx on the merged MT1_popc25.pdb file, but pdb2gmx 
> (option 0: GROMACS ff) did not recognize POPC residue. I also tried 
> merging popc_processed.top (obtained when running grompp for the hole in 
> the bilayer) and MT1_z.top (obtained by pdb2gmx acting upon MT1_z.pdb), 
> but that did not work.
> 
> 
> 
> 
>  What exactly is missing from my MT1_popc25.top file:

there is no protein!


> 
> ; topology for MT1rmmlpHf_z in POPC bilayer with 114 lipids and 2460 SPC waters
> #include "ffgmx.itp"
> #include "popc.itp"
> 
> #ifdef POSRES
> #include "posre.itp"
> #endif
> 
> #ifdef FLEX_SPC
> #include "flexspc.itp"
> #else
> #include "spc.itp"
> #endif
> 
> [ system ]
> ; name
> MT1rmmlpHf_z in POPC bilayer with 114 lipids and 2460 water molecules
> 
> [ molecules ]
> ; name  number
> Protein 1
> POPC    114
> SOL     2460
> 
> I appreciate your advice.
> 
> Martina
> 
> David van der Spoel wrote:
> 
> >There is no protein in your topology.
> >
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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