[gmx-users] Displacement of coordinates by an order of magnitude by pdb2gmx

[Peter Stern]

The pdb file is in Angstroms.  Gromacs uses nanometers, thus the decrease by a factor of 10 -> 1nm = 10A

Peter

-----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 Anna Lohning
Sent: Friday, July 07, 2017 6:07 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] Displacement of coordinates by an order of magnitude by pdb2gmx

Hi
I've looked all through the GROMACS documentation re actions of the PDB2GMX command but I cant' see a reference to why it appears to change the coordinates of the input .pdb file (basically decreasing them by an order of magnitude). Is this normal? When grepping out your docked ligands this causes problems later when you put the ligand coordinates back in prior to creating the box, having to then alter those coordinates in the same manner. I am obviously missing some important information!  (I using Gromacs 5.0.4) Kind regards & many thanks/Anna


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