Emine Deniz Tekin wrote:
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
Nor should you expect it to. Building the parent force field does not give you
a topology describing some molecular system.
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
See the manual, section 5.6.4. The contents and format are discussed at length.
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.
If you want free help, you will have to do substantially better than "it was not
sufficient." What is not clear? What have you tried and what was the result?
If you want free help, you've got to demonstrate a willingness to do some work
on your own.
-Justin
Best regards
Deniz
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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