[gmx-users] Issue with the PDB generated after topology

Khadija Amine kh.amine1 at gmail.com
Sun Jul 2 17:17:58 CEST 2017

Dear Gromacs users,

I'm running a protein complex simulations with the gromacs software.

My complex is two different proteins named chain A (1-166 aa) and chain B
(55-131)with 3 ions and one ligand.

I have produced the topology for the every component of my complex using
pdb2gmx program.

However, when I have visualised the resulted pdb file with pymol, I can see
the two displayed proteins but the amino acids sequence is not complete. I
can see the chain A and not the chain B.

Please, how can I fix this issue?

*Khadija Amine*
Ph.D. Biology and Health
Biochemistry & Bioinformatics
Phone: 33339584

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