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

[Brett]

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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Re: [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  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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> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
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