[gmx-users] lipopeptide problem

Emine Deniz Tekin edeniztekin at gmail.com
Wed Mar 16 22:53:40 CET 2011


I am using the GROMACS 4.5.3 version with GROMOS53a6 force field. I
simulated a peptide before but this is the first time I am trying to combine
a lipid with a peptide (to get a lipo-peptide). I would be really happy if
you could help me out with the following question

I am tring to create a louroic acid connected to and an 8-redidue peptide.
To create residues, I used ARGUSLAB . For the louric acid I used BERGER
lipid parameters. Then, as described in KALP-15 in DPPC tutorial, I combined
ffbonded.itp and ffnonbonded.itp with lipid.itp. I also adjusted the
topol.top files as described in the manual. But this procedure did not yet
give me an attached louric acid and peptide. I still have to play with the
aminoacids.hdb, aminoacids.rtp, residuetypes.dat, atomtypes.atp, and
specbond.dat files. I would appreciate if you could let me know how to
modify these files, especially the aminoacids.hdb file. I tried several
things but it not work. Note that, I applied the suggestions in
but it was not sufficient.

Best regards

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