[gmx-users] echo "15 y 1 1 ......" failed for "gmx pdb2gmx" with "-merge"

Zhang, Cheng c.zhang.11 at ucl.ac.uk
Thu Jul 9 16:50:32 CEST 2015

Dear GROMACS researchers,

I was trying to assign the protonation status in one go by the following:

echo "15 y 1 1 1 ......" | gmx pdb2gmx -f HC_A227E.pdb -o HC_A227E_processed.gro -water spce -inter -ignh -merge interactive

In the commandline above, the "......" means the protonation status for different chargeable residues.

Because I have an inter-chain disulfide bond in my two-chain protein, I have to use "-merge" to keep this inter-chain disulfide bond. The second interactive prompt is to ask if I want to merge these two chains. So my answer is "y". However, it seems that the "echo" command could not be recognised if "y" is used and I got the following error message:

Merge chain ending with residue CYS214 (chain id 'L', atom 3258 SG) and chain starting with

residue GLU215 (chain id 'H', atom 3263 N) into a single moleculetype (keeping termini)? [n/y]


Program gmx, VERSION 5.0.4

Source code file: /home/lanselibai/Cheng/gromacs-5.0.4/src/gromacs/gmxpreprocess/pdb2gmx.c, line: 1571

Fatal error:

Error reading from stdin

For more information and tips for troubleshooting, please check the GROMACS

website at http://www.gromacs.org/Documentation/Errors


So can I ask how to use "echo" to merge chains so that I can assign protonation status in one go?

Thank you very much.

Yours sincerely


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