[gmx-users] on CHARMM-GUI produced lipid bilayer for gromacs use

[Tsjerk Wassenaar]

Hi Brett,

The CHARMM-GUI also provides the .top file. You can use that and the PDB
(it doesn't need to be .gro) to run grompp.

Cheers,

Tsjerk

On Thu, Sep 17, 2015 at 5:06 AM, Brett <brettliu123 at 163.com> wrote:

> Dear All,
>
>
> After I got the membrane protein PDB with the membrane part packed in
> lipid bilayer by the lipid bilayer builder of CHARMM-GUI, will you please
> let me know how to get the inputs for the gromacs next step MD process？ For
> example， if I wand to go directly to the nvt equilibration step with the
> CHARMM-GUI produced PDB, the command in the lysozyme tutorial is "gmx
> grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr". Then will you please
> let me know how to get the input *.gro and *.top file in order to get the
> *.tpr file? Or for the  CHARMM-GUI produced PDB, I delete all the H2O, and
> then start from the pdb2gmx step with the PDB file containing only the
> membrane protein and the lipid bilayer? But in this way it seems the sides
> of the lipid bilayer will also be packed in H2O.
>
>
> I am looking forward to getting a reply from you.
>
>
> Best regards.
>
>
> Brett
>
>
>
>
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.