[gmx-users] lipopeptide problem

Justin A. Lemkul jalemkul at vt.edu
Wed Mar 16 23:00:14 CET 2011

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.


> Best regards
> Deniz


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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