Volker Wirth wrote:
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?
Well, if you replace parameters from ffG53a6 with those of the
*deprecated* ffgmx, you won't be using the ffG53a6 force field any
more. Besides, the Gromos parameters for lipids do not represent the
lipid properties as well as the Berger parameters from Tieleman's site,
so I don't know exactly why you are doing this...
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?
What you need to do is read a bit about including .itp files (Chapter 5
of the manual), and search the list archive, since membrane questions
are quite common. Here are the basics:
1. Append the lipid parameters to your desired force field *nb.itp and
*bon.itp files. I believe the lipid.itp atom types come from the Gromos
force fields, so you can append them to the appropriate force field
there (and I have seen many people use the Gromos96 FF's in literature
simulations of membrane proteins), or you can follow Chris Neale's
elegant setup for use with OPLS parameters (search the list archive).
2. Then, you will need a simple topology file, calling (for example)
"modified_FF.itp" as the force field topology to which you have appended
your lipid parameters.
#include "modified_FF.itp"
#include "dppc.itp"
#include "spc.itp"
[ molecules ]
DPPC x
SOL y
Hopefully that makes sense. Do check the archive, there are lots of
messages about this type of thing.
-Justin
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
--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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