Re: [gmx-users] Respect waters in crystallographic pdb file?
And what about genion? Suppose I have to add some ions to the system to neutralize, so I use the following command: genion -s S_ion.tpr -o S_sol.gro -p S_sol.top -nn 1 -nname CL SOL Is there a chance that this replaces one of the original crytallographic waters with the CL? 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=windows-1252; format=flowed 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 -- == 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == 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 --- [http://5.cim.co.cu/cim.gif] -- 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.
Re: [gmx-users] Respect waters in crystallographic pdb file?
On 8/20/15 10:06 AM, Jorge Fernandez de Cossio Diaz wrote: And what about genion? Suppose I have to add some ions to the system to neutralize, so I use the following command: genion -s S_ion.tpr -o S_sol.gro -p S_sol.top -nn 1 -nname CL SOL Is there a chance that this replaces one of the original crytallographic waters with the CL? There's always a chance; it's random. It's easy to check and if you get an undesired result, just change the value of -seed. Or distinguish the crystal waters as some other [moleculetype] name, which requires some topology hacking. -Justin 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=windows-1252; format=flowed 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 -- == 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == 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 --- [http://5.cim.co.cu/cim.gif] -- == 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
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, 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 advance. Best, cossio --- [http://5.cim.co.cu/cim.gif] -- 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.
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 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 -- == 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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- 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.
