Re: [gmx-users] Trjconv PDB files define solvent as "ATOM"?

On 20/03/2012 5:10 AM, John Ladasky wrote: I am trying to import PDB file snapshots from a GROMACS 4.5.4-generated trajectory into other software tools -- specifically, Biopython. I generate the snapshots using trjconv in GROMACS. I am interested in the water molecules from my solvent box, so

Re: [gmx-users] Trjconv PDB files define solvent as "ATOM"?

Hi John, Maybe it was laziness, maybe it was the realization that the distinction between atom and hetatm is a bit awkward that caused the developers not to bother with it. It also doesn't relate to your problem, probably. There are non-standard residues and covalently bound ligands that are happi

Re: [gmx-users] Trjconv PDB files define solvent as "ATOM"?

Following up to myself: Looking back through the archives, I have learned that the issue of solvent atoms being exported from trjconv into PDB files as "ATOM" rather than as "HETATM" is an issue that was raised fully six years ago. http://www.mail-archive.com/gmx-users@gromacs.org/msg00405.ht

[gmx-users] Trjconv PDB files define solvent as "ATOM"?

I am trying to import PDB file snapshots from a GROMACS 4.5.4-generated trajectory into other software tools -- specifically, Biopython. I generate the snapshots using trjconv in GROMACS. I am interested in the water molecules from my solvent box, so I do not discard them. When trjconv promp