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

[ZHANG Cheng]

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


I think "echo" only works for choosing the force field, but not work for the charge assignment. 


e.g. when I use:


echo 15 0 0 0 0 | gmx pdb2gmx  -f protein.pdb -o protein_processed.gro -water spce  -inter  -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:     gmx pdb2gmx, version 2020-beta2
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 130)
Fatal error:
Answer me for res GLUTAMINE 3!





------------------ Original ------------------
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?