VMD-L Mailing List

From: Ramon Mendoza Uriarte (ramendoza_at_uchicago.edu)
Date: Sat Mar 20 2021 - 23:15:56 CDT

Hello VMD Community,

I loaded a molecule with its respective .psf and .coor files, where the .coor file was read as a NAMD Binary Coordinates file. I then wanted to write out the pdb file; for example, by doing the following in the TkConsole:

set all [atomselect top "all"]
$all writepdb new.pdb

However, I found it surprising that this yields slightly different coordinates and box dimensions. For instance:

>From .coor: (-12.171550750732422, 5.363558769226074, -15.094483375549316), (-11.626058578491211, 4.931212425231934, -15.867215156555176),
                      (-12.769146919250488, 6.002536773681641, -15.656786918640137) <--- A small subset of all the coordinates
                      cellBasisVector1 87.59627914428711 0 0
                      cellBasisVector2 0 88.96563339233398 0
                      cellBasisVector3 0 0 97.37928009033203
                      cellOrigin 0.1676909178495407 0.361166387796402 0.04699717089533806

>From new.pdb: (-12.17199993133545, 5.363999843597412, -15.093999862670898), (-11.62600040435791, 4.931000232696533, -15.866999626159668),
                            (-12.769000053405762, 6.002999782562256, -15.656999588012695) <--- A small subset of all the coordinates
                            cellBasisVector1 87.59599685668945 0 0
                            cellBasisVector2 0 88.96599960327148 0
                            cellBasisVector3 0 0 97.37999725341797
                            cellOrigin 0.16769009828567505 0.36116769909858704 0.04699849709868431

So far, I have tried a Google and VMD archive search; however, I have not determined why this occurred. Additionally, I am using VMD for LINUXAMD64, version 1.9.4a51. Any comments on why this occurred would be appreciated.

Thank you,
Ramon