[gmx-users] pdb2gmx: intra-chain disulfide bond missing problem

Zhang, Cheng c.zhang.11 at ucl.ac.uk
Wed May 20 18:17:42 CEST 2015

Dear GROMACS users,

Can I ask a disulfide bond question if possible?

The link below is my protein L50K.pdb with 5 disulfide bonds.


After using

gmx pdb2gmx -f L50K.pdb -o L50K_processed.gro -water spce -inter -ignh -merge interactive

one of the disulfide bonds (i.e. Heavy Chain, HC 236-310) does not show up in the interactive prompt. As a result, they become -SH instead of -S-S- in the output .gro file (also in the link).

I tried to search solutions but could not find the answer for this intra-chain disulfide bond missing problem. Could you please help me?

Thank you very much.

Yours sincerely


(I was trying to upload the PDB file by attachment. But it seems that the mail has not been approved. So I use a link instead.)

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