[email protected] 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
--
========================================
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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