[gmx-users] Automatically assign the protonation states for pdb2gmx

Mark Abraham mark.j.abraham at gmail.com
Sat Feb 22 09:45:47 CET 2020


Hi,

Echo works just fine - you just need a way to script what input it injects
to the stdin of pdb2gmx. That's logic you need for any solution so is
probably easiest. The expect tool may be another option.

Mark

On Fri., 21 Feb. 2020, 21:41 ZHANG Cheng, <272699575 at qq.com> wrote:

> I want to run more than 300 MD, each with a different PDB (more precisely,
> variants derived from a same wild type). I need to manually assign the
> protonation states using the "-inter" option every time, which is
> impossible for more than 300 times.&nbsp;
>
>
> gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce&nbsp;
> -inter&nbsp; -ignh -merge interactive&nbsp;
>
>
> The protonation states come from the pdb2pqr website. Is there an
> alternative way to obtain the .gro file by providing the necessary inputs
> (e.g. pdb, protonations), so that I can batch obtain the 300 corresponding
> .gro files?
>
>
> I know the "echo" could not work for the charge assignment.
>
>
> It would be ultimately possible if I can understand the fundamental codes
> behind "pdb2gmx", then write a batch code to process multiple PDB files at
> once. But is there a simpler route?
> --
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