Thanks Dan. I overlooked the ptraj option, that actually makes the process a bit easier.
Best,
Jesper
On Apr 30, 2012, at 7:52 AM, Daniel Roe wrote:
> Hi,
>
> On Mon, Apr 30, 2012 at 2:42 AM, Jesper Sørensen <jesorensen.ucsd.edu> wrote:
>> 1) Use "ambpdb" in AMBER and you get a pqr file with radii from the "%FLAG RADII" section of the prmtop. So this seems okay and in accordance with the PBSA protocol.
>> 2) You can also go the long and complicated way and create a PDB file of a snapshot from your simulation (using e.g. VMD). Then feed this into pdb2pqr and ask for the AMBER radii. However, this will actually give you the LJ radii from the Amber ff94 in the pqr file.
>
> You can also use ptraj/cpptraj to write PQR files with GB radii:
>
> PTRAJ: trajout struct.pqr pdb dumpq
> CPPTRAJ: trajout struct.pqr pdb dumpq multi
>
> The 'multi' keyword in cpptraj is for multiple frame input
> trajectories, and makes it so 1 file is printed for every frame;
> otherwise the default behavior is to have all structures in 1 PDB file
> separated by MODEL/ENDMDL keywords.
>
> -Dan
>
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Received on Wed May 02 2012 - 08:30:03 PDT
