[gmx-users] Including itp files

[Volker Wirth]

Hi all,
maybe these are stupid questions, but in the moment I'm a bit in a
files' mess, so I apologize for that...

I want to use a lipid bilayer pdb from the Tieleman group, let's say
http://moose.bio.ucalgary.ca/files/dppc64.pdb, and the first goal is
to get the structure "into" GROMACS and to see if it works. If I run
pdb2gmx -ignh -ff G53a6 -f dppc64.pdb -o lipids.pdb -p lipids.top
I get a problem with the rtp file, "Atom N4 in residue DPPC 1 not
found in rtp entry with 50 atoms while sorting atoms", , but it works
with gmx, so

1) may I just replace the [DPPC] part of ffG53a6.rtp with the
equivalent part of ffgmx.rtp or have I to edit the G53a6 file so that
the first columns are the same?

It works with the gmx force field and I can run editconf and genbox.
But when I use
grompp_d -f em.mdp -c lipids_b4em.pdb -p lipids.top -o lipids_em.tpr
the program is determined by too many warnings like "WARNING 1 [file
"lipids_A.itp", line 69]: No default Bond types, using zeroes" so I
think, this is the place, where the itp files (lipid.itp, dppc.itp),
offered besides the pdb should do some job here. But

2) how will I get these files involved into my simulation?

I hope, you understand my problem, as for myself it is not yet really
clear, what e.g. the itp file will actually do within the process...

Best
Volker

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Volker Wirth
Center for Medical Physics and Technology
Biophysics Group
FAU Erlangen-Nuremberg

Email: vwirth%at%biomed.uni-erlangen.de
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