[gmx-users] [Fwd: Re: Grompp problems upon embedding a receptor into POPC]
David van der Spoel
spoel at xray.bmc.uu.se
Thu Nov 6 12:49:00 CET 2003
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
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
[ system ]
MT1rmmlpHf_z in POPC bilayer with 114 lipids and 2460 water molecules
[ molecules ]
; name number
I appreciate your advice.
David van der Spoel wrote:
>There is no protein in your topology.
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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