AW: [gmx-users] lipopeptide problem
frausch at ipb-halle.de
Thu Mar 17 08:28:02 CET 2011
If you want the lipid connected to the amino acid, i think it would be a good idea to add a new residue type to aminoacids.rtp which contains both, your lipid and the amino acid its connected to. You can start from the rtp entry of the amino acid and add the lipid parameters. After doing that, you can use pdb2gmx to build the topology for the whole system even without any need to adjust the .top afterwards. The link you gave is the right place to get a "route" for this intent.
Von: gmx-users-bounces at gromacs.org im Auftrag von Emine Deniz Tekin
Gesendet: Mi 16.03.2011 22:53
An: gmx-users at gromacs.org
Betreff: [gmx-users] lipopeptide problem
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.
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