[gmx-users] Lipid bilayer parameters

[Tsjerk Wassenaar]

Hi Nagaraju,

It looks like you miss the first atom in the pdb file (which should be
a C1). In addition, check your box, since there's something wrong with
that too, according to the grompp output.

Hope it helps,

Tsjerk

On 7/23/05, David <spoel at xray.bmc.uu.se> wrote:
> On Sat, 2005-07-23 at 05:20 -0700, naga raju wrote:
> > Dear gmx-users,
> >                 I built a lipid bilayer (72 lipid
> > molecules and 2376 water molecules) by taking one
> > lipid molecule from the dppc.pdb file in website:
> > http://moose.bio.ucalgary.ca/index.php?page=Downloads
> >  I downloaded dppc.itp and lipid.itp files from the
> > above link. when i used the grompp command, it shows
> > the following error.
> >
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C1 - C2)
> this is bad.
> fix your top or pdb file such that they match.
> 
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C2 - N4)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (N4 - C5)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C5 - C6)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C6 - O7)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (O7 - P8)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (P8 - O9)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (O9 - O10)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (O10 - O11)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (O11 - C12)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C12 - C13)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C13 - O14)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (O14 - C15)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C15 - O16)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (O16 - C17)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C17 - C18)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C18 - C19)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C19 - C20)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C20 - C21)
> > Warning: atom names in dppc.top and bbww.pdb don't
> > match (C21 - C22)
> > (more than 20 non-matching atom names)
> > WARNING 1 [file "dppc.top", line 26]:
> >   9096 non-matching atom names
> >   atom names from dppc.top will be used
> >   atom names from bbww.pdb will be ingnored
> >
> > double-checking input for internal consistency...
> > ERROR: One of the box vectors is shorter than twice
> > the cut-off length. Increase the box size or decrease
> > rlist.
> > There was 1 warning
> >
> >
> > How can be the problem solved?
> > Here i gave my dppc.top file:
> >
> > #include "ffgmx.itp"
> > #include "lipid.itp"
> > #include "dppc.itp"
> > #include "alm.itp"
> > #include "ions.itp"
> >
> > #ifdef FLEX_SPC
> > #include "flexspc.itp"
> > #else
> > #include "spc.itp"
> > #endif
> >
> > [ system ]
> > ; name
> > Alm on surf + relaxed popc
> >
> > [ molecules ]
> > ; name        number
> > DPPC    72
> > SOL     2376
> >
> >
> >                  Thank you
> >                                   nagaraju
> >
> >
> >
> >
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> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. 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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