Hi Tsjerk:
But, i think the problems is that pdb2gmx program see the membrane
how a protein and it tries to tie the peptide with the membrane. The
topology of dppc membrane appear in the ffG53a5.rtp file of gromacs.
What can i do? Should i create a peptide.top file and include it a
lipid.itp and dppc.itp file?
The lipid.itp file i took from Dr. Peter tieleman site is for GROMOS87
forcefield and i use GROMOS96 forcefield.
Thanks for the help,
Maite
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