[gmx-users] Question Re. KALP-15 in DPPC tutorial

[Justin Lemkul]

On 1/24/14, 10:30 PM, jhosamelly wrote:
> 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.
>
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html
>
>
> 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
> ffnonbonded.itp.
>
> 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
>

There are multiple steps in this process; it encompasses most of the second 
entitled "1. Orient the protein and membrane."

> "(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
>
> Fatal error:
> Unknown atomtype HW
>

 From 
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html:

"Non-bonded interactions involving atom type HW are also present; since these 
are all zero you can delete these lines as well, or otherwise rename HW as H to 
be consistent with the GROMOS96 53A6 naming convention. If you do not rename 
these lines or remove them, grompp will later fail with a fatal error."

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

==================================================