Hi GROMACS Users, 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 http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field, but it was not sufficient. Best regards Deniz
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