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

[Mark Abraham]

Hi,

On Sat, 22 Feb 2020 at 14:07, ZHANG Cheng <272699575 at qq.com> wrote:

> Thank you Mark! Sorry could you please explain the details of "stdin" of
> "pdb2gmx"? Is there a link for it?
>

The stdin stream is a fundamental concept in how unix terminals work. The
echo tool fills that stream for pdb2gmx to consume. This is a pattern
followed by thousands of tools.


> I think "echo" only works for choosing the force field, but not work for
> the charge assignment.&nbsp;
>
>
> e.g. when I use:
>
>
> echo 15 0 0 0 0 | gmx pdb2gmx&nbsp; -f protein.pdb -o
> protein_processed.gro -water spce&nbsp; -inter&nbsp; -ignh -merge
> interactive
>
>
> I got error message:
>
>
> Which GLUTAMINE type do you want for residue 3
> 0. Not protonated (charge 0) (GLN)
> 1. Protonated (charge +1) (QLN)
> Type a number:
> -------------------------------------------------------
> Program:&nbsp; &nbsp; &nbsp;gmx pdb2gmx, version 2020-beta2
>

Please install a proper version of GROMACS, not a pre-release one, which we
asked you not to use for scientific work.


> Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 130)
> Fatal error:
>

That's probably because you haven't given enough numbers to echo to satisfy
the needs of pdb2gmx, but I can't tell on the information you've given.

Mark


> Answer me for res GLUTAMINE 3!
>
>
>
>
>
> ------------------&nbsp;Original&nbsp;------------------
> From:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
> Date:&nbsp;Sat, Feb 22, 2020 04:39 AM
> To:&nbsp;"gromacs.org_gmx-users"<gromacs.org_gmx-users at maillist.sys.kth.se
> &gt;;
> Cc:&nbsp;"ZHANG Cheng"<272699575 at qq.com&gt;;
> Subject:&nbsp;Automatically assign the protonation states for pdb2gmx
>
>
>
> 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.
>
>
> gmx pdb2gmx -f protein.pdb -o protein_processed.gro -water spce&nbsp;
> -inter&nbsp; -ignh -merge interactive
>
>
> 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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