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

[David van der Spoel]

-----Forwarded Message-----

From: "Martina Bertsch, PhD" <mbe404 at lulu.it.northwestern.edu>
To: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: Grompp problems upon embedding a receptor into POPC
Date: 06 Nov 2003 05:26:23 -0600

Hello, David.

Thanks for the quick reply. I know the error message: "... No 
moleculetype Protein" suggests that there is no protein in my topology, 
but I am a bit confused: I do include the newest ffgmx.itp in my 
MT1_popc25.top file, which I thought should contain forcefield 
parameters for both proteins and lipids.

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:

; 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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