[gmx-users] atom numbering

Peter Stern peter.stern at weizmann.ac.il
Sun Dec 6 14:45:09 CET 2015

Justin already answered your question five days ago:
Use the -norenum option for pdb2gmx


-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Marta Wisniewska
Sent: Sunday, December 06, 2015 2:03 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] atom numbering

Dear Gromacs users,

My problem focus on number order. I am preparing my system to md. In my pdb file I made a some modifications (delete chains or ligand compounds).
During preparation of topology and gro file, the residue number ordering is changed. Is there any possibility to preserve number ordering from pdb file during pdb2gmx transfer?

Thank you in advance,
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