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 Cheng -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
