[gmx-users] Question Re. KALP-15 in DPPC tutorial
ducut_melsarose at yahoo.com
Sat Jan 25 04:30:08 CET 2014
I'm now doing the GROMACS tutorial KALP-15 in DPPC
I followed everything that is said needed to be changed in the topol.top,
lipid.itp, ffbonded.itp, ffnonbonded.itp . Or at least I think so.
I copied the [atom type] section from the tutorial, since as what it says
the one from lipid.itp lacks atm.no. column, to the ffnonbonded.itp.
I copied [ nonbond_params ] from the lipid.itp, except the section ";;
parameters for lipid-GROMOS interactions." , to the [ nonbond_params ] at
I copied [ pairtypes ] from lipid.ito to [ pairtypes ] at ffnonbonded.itp.
I copied the [ dihedraltypes ] from lipid.itp to the ffbonded.itp
but the when I tried to follow this
"We have already aligned the KALP peptide using editconf. The bilayer lies
in the x-y plane, with the normal along the z-axis. Convert the dppc128.pdb
to .gro format with editconf and remove the initial periodicity. The latter
step is easily accomplished through the use of trjconv:"
the command I used is editconf -f dppc128.pdb -o dppc128.gro
I don't know how to "remove the initial periodicity" so I continued and
typed the next command
"(1) Generate a .tpr file for a DPPC-only system using grompp. You can use
any valid .mdp file and a topology corresponding to pure DPPC. An example
.mdp file can be found here and such a topology can be found here. Note how
simple the topology is. It includes dppc.itp and spc.itp to read parameters
for DPPC and water; it's that simple! Run grompp:
grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr"
I get fatal error
Unknown atomtype HW
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