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-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Anna Lohning Sent: Friday, July 07, 2017 6:07 AM To: gmx-us...@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 -- 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. -- 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.
