Re: [gmx-users] Respect waters in crystallographic pdb file?

, cossio -- Message: 2 Date: Mon, 17 Aug 2015 14:14:28 -0400 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Respect waters in crystallographic pdb file? Message-ID: 55d22484.9030...@vt.edu Content-Type: text/plain; charset=windows-1252

Re: [gmx-users] Respect waters in crystallographic pdb file?

Thanks. Best, cossio -- Message: 2 Date: Mon, 17 Aug 2015 14:14:28 -0400 From: Justin Lemkul jalem...@vt.edu To: gmx-us...@gromacs.org Subject: Re: [gmx-users] Respect waters in crystallographic pdb file? Message-ID: 55d22484.9030...@vt.edu Content-Type: text/plain; charset

Re: [gmx-users] Respect waters in crystallographic pdb file?

I haven't tried that before. May be you can open the .gro files before and after genbox with a text editor. Then, check those water molecules? Those water molecules might have the same residue id. On Mon, Aug 17, 2015 at 1:42 PM, Jorge Fernandez de Cossio Diaz cos...@cim.sld.cu wrote: Hi all,

[gmx-users] Respect waters in crystallographic pdb file?

Hi all, I have a crystallographic PDB file which comes some waters molecules. I want to run an MD simulation which includes those water molecules. After generating the topology file (which includes the waters) and defining the box shape, I fill the box with solvent using genbox. At this point

Re: [gmx-users] Respect waters in crystallographic pdb file?

On 8/17/15 1:42 PM, Jorge Fernandez de Cossio Diaz wrote: Hi all, I have a crystallographic PDB file which comes some waters molecules. I want to run an MD simulation which includes those water molecules. After generating the topology file (which includes the waters) and defining the box