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

Justin Lemkul jalemkul at vt.edu
Mon Aug 17 20:14:40 CEST 2015

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
> shape, I fill the box with solvent using genbox. At this point it becomes
> impossible to track down visually where the water molecules are. My question
> is if the file that genbox outputs still contains the crystallographic water
> molecules? Or are they replaced by the molecules added by genbox? Thanks in

They should be in the same place they always were (unless you've modified the 
box dimensions, in which case the coordinates of everything get changed).  But 
genbox shouldn't delete waters that were already present.  The crystallographic 
waters should always be the first ones written after e.g. the protein.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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