[gmx-users] problems with KALP-15 IN DPPC tutorial

Justin A. Lemkul jalemkul at vt.edu
Mon Jan 30 14:53:52 CET 2012

scaprari at uniroma3.it wrote:
> Hello,
> I have got Gromacs version 4.0.7 and I' m trying to simulate and extend
> one patch of membrane (dppc128.pdb)downloaded by the website. I am
> following the gromacs tutorial "KALP-15 IN DPPC" but I have some problems
> during "step 2: modify the topology" because I need to find the following
> files:
> aminoacids.rtp
> aminoacids.hdb
> aminoacids.c.tdb
> aminoacids.n.tdb
> aminoacids.r2b
> aminoacids.vsd
> ff_dum.itp
> ffnonbonded.itp
> ffbonded.itp
> forcefield.itp
> ions.itp
> spc.itp
> watermodels.dat
> that are reported in the tutorial. I can't find them in any directory.
> Could it depend on the different Gromacs versions? Any suggestion will be
> appreciated.

Yes.  The tutorial states that it is designed for Gromacs 4.5.x; older versions 
have completely different force field organization.



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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