RE: [gmx-users] creating a solvent box
Is there something about the water molecule that is different to any standard H2O? If not, then simply use: genbox_d -cs -box 4.0 6.0 4.0 -maxsol 3200 Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9909 9304 - When the only tool you own is a hammer, every problem begins to resemble a nail. From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On Behalf Of Eric Shamay Sent: Tuesday, 21 September 2010 10:17 AM To: gmx-users@gromacs.org Subject: [gmx-users] creating a solvent box This may very well be a simple problem, but I have found little in the way of documentation that helped me get it to work: I'd like to form a box (4x6x4 nm^3) filled with 3200 water molecules. I'd like to use the water model specified in sw.itp (polarizable & flexible). In the working directory I have a pdb file that specifies exactly the final system that I want to use, but I cannot generate a .gro file from this pdb file in order to run a simulation. I've tried 2 routes to accomplish this: 1) pdb2gmx - I've attempted to use this program as follows: 'pdb2gmx_d -f sw_box.pdb -o sw_box.gro -i sw.itp' This reports a fatal error: Residue 'SW' not found in residue topology database Because the sw.itp file defines SW as the molecule name, and again as the residue name, I assumed that's what I'd want to appear in my pdb file as well. I've tried every combination of force fields and water model to see if that would do anything, but to no avail. 2) genbox - I tried to generate a solvent box using the pdb file as the solvent definition: 'genbox_d -cs sw_box.pdb -box 4.0 6.0 4.0 -maxsol 3200' This made it look as though it was running, but after a very long time it did not return and produce a .gro file I could use. It's as if the program just hung or got stuck in some overly complicated solvation routine. I realize that the SW residue is not defined in the standard force fields, and so that's why I want to include sw.itp. Is there a way to generate this box? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] creating a solvent box
Eric Shamay wrote: This may very well be a simple problem, but I have found little in the way of documentation that helped me get it to work: I'd like to form a box (4x6x4 nm^3) filled with 3200 water molecules. I'd like to use the water model specified in sw.itp (polarizable & flexible). In the working directory I have a pdb file that specifies exactly the final system that I want to use, but I cannot generate a .gro file from this pdb file in order to run a simulation. I've tried 2 routes to accomplish this: 1) pdb2gmx - I've attempted to use this program as follows: 'pdb2gmx_d -f sw_box.pdb -o sw_box.gro -i sw.itp' This reports a fatal error: Residue 'SW' not found in residue topology database Because the sw.itp file defines SW as the molecule name, and again as the residue name, I assumed that's what I'd want to appear in my pdb file as well. I've tried every combination of force fields and water model to see if that would do anything, but to no avail. Since you've already got sw.itp, then there's no point at all in running pdb2gmx, whose sole purpose is to create topologies. Since you've got that, your life should be easy: #include (force field) #include "sw.itp" [ system ] SW [ molecules ] SW 3200 2) genbox - I tried to generate a solvent box using the pdb file as the solvent definition: 'genbox_d -cs sw_box.pdb -box 4.0 6.0 4.0 -maxsol 3200' This made it look as though it was running, but after a very long time it did not return and produce a .gro file I could use. It's as if the program just hung or got stuck in some overly complicated solvation routine. I realize that the SW residue is not defined in the standard force fields, and so that's why I want to include sw.itp. Is there a way to generate this box? Above you state that sw_box.pdb contains the system you want. If that's the case, there's no need for genbox at all. Use sw_box.pdb as your coordinate file input into grompp in conjunction to the skeleton topology I have shown above. If your goal is simply to obtain a .gro file, just use editconf. But do note that there is no requirement whatsoever that you have to use .gro format. Most Gromacs tools are extremely flexible, and a .pdb file will work just fine. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] creating a solvent box
This may very well be a simple problem, but I have found little in the way of documentation that helped me get it to work: I'd like to form a box (4x6x4 nm^3) filled with 3200 water molecules. I'd like to use the water model specified in sw.itp (polarizable & flexible). In the working directory I have a pdb file that specifies exactly the final system that I want to use, but I cannot generate a .gro file from this pdb file in order to run a simulation. I've tried 2 routes to accomplish this: 1) pdb2gmx - I've attempted to use this program as follows: 'pdb2gmx_d -f sw_box.pdb -o sw_box.gro -i sw.itp' This reports a fatal error: Residue 'SW' not found in residue topology database Because the sw.itp file defines SW as the molecule name, and again as the residue name, I assumed that's what I'd want to appear in my pdb file as well. I've tried every combination of force fields and water model to see if that would do anything, but to no avail. 2) genbox - I tried to generate a solvent box using the pdb file as the solvent definition: 'genbox_d -cs sw_box.pdb -box 4.0 6.0 4.0 -maxsol 3200' This made it look as though it was running, but after a very long time it did not return and produce a .gro file I could use. It's as if the program just hung or got stuck in some overly complicated solvation routine. I realize that the SW residue is not defined in the standard force fields, and so that's why I want to include sw.itp. Is there a way to generate this box? -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists