Re: [gmx-users] Docking with PyMol and using Gromacs
Dallas B. Warren a écrit : Coordinate files like pdb and gro aren’t used by GROMACS to provide any bonding information. That is what the topology files are for. So their “presence” in your pdb isn’t an issue. Actually, what is probably happening is that PyMol is guessing the bonds presence, based on the distance between atoms, and displaying it (which is what VMD does as well). So the bonds aren’t actually there at all in the pdb file. VMD can read/write CHARMM/NAMD topology files (namely psf files). If your problem is *just* a visualization artefact, you can load your structure in VMD, write a psf file and delete the unwanted bonds (this does not require a specific forcefield). You can also combine 2 psf files (1 for your protein and 1 for your ligand), that require some basic knowledge of TCL though. After that, you just have to load the topology abd the coordinates: vmd -psf topology.psf -pdb coordinate.pdb You won't see any weird bonds. Nicolas Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - 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 *Gunnar Widtfeldt Reginsson *Sent:* Thursday, 12 November 2009 10:13 AM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] Docking with PyMol and using Gromacs Hi. I am a new user of Gromacs. My question is both PyMol and Gromacs related. I tried the PyMol users mailing list but couldn't find anything. I have a small organic molecule that I am inserting into DNA in pymol. I have the DNA as one pdb file and the organic molecule as another pdb file. I open the DNA file in pymol and then load the organic molecule. After docking the organic molecule I write save name.pdb When viewing the name.pdb file in pymol there are some bonds between the organic molecule and the DNA that I don't want. Somehow pymol creates them and I don't see those bonds in the name.pdb file when I open it in a text reader. I then create a .gro file with pdb2gmx of the DNA.pdb and a .gro file of the organic molecule with topolbuilder 1.2 , and unite those .gro files and convert into a .pdb with editconf The newly created pdb file still has those unwanted bonds. My question is: Can I ignore those bonds? If not, how can I prevent pymol making those bonds? Thanks. attachment: nicolas_sapay.vcf-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Docking with PyMol and using Gromacs
With VMD it's even simpler: use dynamic bonds. Ran. Nicolas Sapay wrote: Dallas B. Warren a écrit : Coordinate files like pdb and gro aren’t used by GROMACS to provide any bonding information. That is what the topology files are for. So their “presence” in your pdb isn’t an issue. Actually, what is probably happening is that PyMol is guessing the bonds presence, based on the distance between atoms, and displaying it (which is what VMD does as well). So the bonds aren’t actually there at all in the pdb file. VMD can read/write CHARMM/NAMD topology files (namely psf files). If your problem is *just* a visualization artefact, you can load your structure in VMD, write a psf file and delete the unwanted bonds (this does not require a specific forcefield). You can also combine 2 psf files (1 for your protein and 1 for your ligand), that require some basic knowledge of TCL though. After that, you just have to load the topology abd the coordinates: vmd -psf topology.psf -pdb coordinate.pdb You won't see any weird bonds. Nicolas Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - 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 *Gunnar Widtfeldt Reginsson *Sent:* Thursday, 12 November 2009 10:13 AM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] Docking with PyMol and using Gromacs Hi. I am a new user of Gromacs. My question is both PyMol and Gromacs related. I tried the PyMol users mailing list but couldn't find anything. I have a small organic molecule that I am inserting into DNA in pymol. I have the DNA as one pdb file and the organic molecule as another pdb file. I open the DNA file in pymol and then load the organic molecule. After docking the organic molecule I write save name.pdb When viewing the name.pdb file in pymol there are some bonds between the organic molecule and the DNA that I don't want. Somehow pymol creates them and I don't see those bonds in the name.pdb file when I open it in a text reader. I then create a .gro file with pdb2gmx of the DNA.pdb and a .gro file of the organic molecule with topolbuilder 1.2 , and unite those .gro files and convert into a .pdb with editconf The newly created pdb file still has those unwanted bonds. My question is: Can I ignore those bonds? If not, how can I prevent pymol making those bonds? Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Docking with PyMol and using Gromacs
This is exactly what I thought. I found out that saving the file with .mol ending in PyMol does not give the unwanted bonds. Thank you all. On Thu, Nov 12, 2009 at 8:49 AM, Ran Friedman r.fried...@bioc.uzh.chwrote: With VMD it's even simpler: use dynamic bonds. Ran. Nicolas Sapay wrote: Dallas B. Warren a écrit : Coordinate files like pdb and gro aren’t used by GROMACS to provide any bonding information. That is what the topology files are for. So their “presence” in your pdb isn’t an issue. Actually, what is probably happening is that PyMol is guessing the bonds presence, based on the distance between atoms, and displaying it (which is what VMD does as well). So the bonds aren’t actually there at all in the pdb file. VMD can read/write CHARMM/NAMD topology files (namely psf files). If your problem is *just* a visualization artefact, you can load your structure in VMD, write a psf file and delete the unwanted bonds (this does not require a specific forcefield). You can also combine 2 psf files (1 for your protein and 1 for your ligand), that require some basic knowledge of TCL though. After that, you just have to load the topology abd the coordinates: vmd -psf topology.psf -pdb coordinate.pdb You won't see any weird bonds. Nicolas Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - 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 *Gunnar Widtfeldt Reginsson *Sent:* Thursday, 12 November 2009 10:13 AM *To:* gmx-users@gromacs.org *Subject:* [gmx-users] Docking with PyMol and using Gromacs Hi. I am a new user of Gromacs. My question is both PyMol and Gromacs related. I tried the PyMol users mailing list but couldn't find anything. I have a small organic molecule that I am inserting into DNA in pymol. I have the DNA as one pdb file and the organic molecule as another pdb file. I open the DNA file in pymol and then load the organic molecule. After docking the organic molecule I write save name.pdb When viewing the name.pdb file in pymol there are some bonds between the organic molecule and the DNA that I don't want. Somehow pymol creates them and I don't see those bonds in the name.pdb file when I open it in a text reader. I then create a .gro file with pdb2gmx of the DNA.pdb and a .gro file of the organic molecule with topolbuilder 1.2 , and unite those .gro files and convert into a .pdb with editconf The newly created pdb file still has those unwanted bonds. My question is: Can I ignore those bonds? If not, how can I prevent pymol making those bonds? Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
[gmx-users] Docking with PyMol and using Gromacs
Hi. I am a new user of Gromacs. My question is both PyMol and Gromacs related. I tried the PyMol users mailing list but couldn't find anything. I have a small organic molecule that I am inserting into DNA in pymol. I have the DNA as one pdb file and the organic molecule as another pdb file. I open the DNA file in pymol and then load the organic molecule. After docking the organic molecule I write save name.pdb When viewing the name.pdb file in pymol there are some bonds between the organic molecule and the DNA that I don't want. Somehow pymol creates them and I don't see those bonds in the name.pdb file when I open it in a text reader. I then create a .gro file with pdb2gmx of the DNA.pdb and a .gro file of the organic molecule with topolbuilder 1.2 , and unite those .gro files and convert into a .pdb with editconf The newly created pdb file still has those unwanted bonds. My question is: Can I ignore those bonds? If not, how can I prevent pymol making those bonds? Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Docking with PyMol and using Gromacs
Gunnar Widtfeldt Reginsson wrote: Hi. I am a new user of Gromacs. My question is both PyMol and Gromacs related. I tried the PyMol users mailing list but couldn't find anything. I have a small organic molecule that I am inserting into DNA in pymol. I have the DNA as one pdb file and the organic molecule as another pdb file. I open the DNA file in pymol and then load the organic molecule. After docking the organic molecule I write save name.pdb When viewing the name.pdb file in pymol there are some bonds between the organic molecule and the DNA that I don't want. Somehow pymol creates them and I don't see those bonds in the name.pdb file when I open it in a text reader. I then create a .gro file with pdb2gmx of the DNA.pdb and a .gro file of the organic molecule with topolbuilder 1.2 , and unite those .gro files and convert into a .pdb with editconf The newly created pdb file still has those unwanted bonds. My question is: Can I ignore those bonds? If not, how can I prevent pymol making those bonds? For the purposes of simulation, a bond is defined in the topology, not the coordinate file. What you are seeing is simply an artifact of the heuristic methods that visualization programs use to guess where bonds should be. -Justin Thanks. -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar 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/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/mailing_lists/users.php
RE: [gmx-users] Docking with PyMol and using Gromacs
Coordinate files like pdb and gro aren't used by GROMACS to provide any bonding information. That is what the topology files are for. So their presence in your pdb isn't an issue. Actually, what is probably happening is that PyMol is guessing the bonds presence, based on the distance between atoms, and displaying it (which is what VMD does as well). So the bonds aren't actually there at all in the pdb file. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@pharm.monash.edu.au +61 3 9903 9167 - 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 Gunnar Widtfeldt Reginsson Sent: Thursday, 12 November 2009 10:13 AM To: gmx-users@gromacs.org Subject: [gmx-users] Docking with PyMol and using Gromacs Hi. I am a new user of Gromacs. My question is both PyMol and Gromacs related. I tried the PyMol users mailing list but couldn't find anything. I have a small organic molecule that I am inserting into DNA in pymol. I have the DNA as one pdb file and the organic molecule as another pdb file. I open the DNA file in pymol and then load the organic molecule. After docking the organic molecule I write save name.pdb When viewing the name.pdb file in pymol there are some bonds between the organic molecule and the DNA that I don't want. Somehow pymol creates them and I don't see those bonds in the name.pdb file when I open it in a text reader. I then create a .gro file with pdb2gmx of the DNA.pdb and a .gro file of the organic molecule with topolbuilder 1.2 , and unite those .gro files and convert into a .pdb with editconf The newly created pdb file still has those unwanted bonds. My question is: Can I ignore those bonds? If not, how can I prevent pymol making those bonds? Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
Re: [gmx-users] Docking with PyMol and using Gromacs
Justin A. Lemkul wrote: Gunnar Widtfeldt Reginsson wrote: Hi. I am a new user of Gromacs. My question is both PyMol and Gromacs related. I tried the PyMol users mailing list but couldn't find anything. I have a small organic molecule that I am inserting into DNA in pymol. I have the DNA as one pdb file and the organic molecule as another pdb file. I open the DNA file in pymol and then load the organic molecule. After docking the organic molecule I write save name.pdb When viewing the name.pdb file in pymol there are some bonds between the organic molecule and the DNA that I don't want. Somehow pymol creates them and I don't see those bonds in the name.pdb file when I open it in a text reader. I then create a .gro file with pdb2gmx of the DNA.pdb and a .gro file of the organic molecule with topolbuilder 1.2 , and unite those .gro files and convert into a .pdb with editconf The newly created pdb file still has those unwanted bonds. My question is: Can I ignore those bonds? If not, how can I prevent pymol making those bonds? For the purposes of simulation, a bond is defined in the topology, not the coordinate file. What you are seeing is simply an artifact of the heuristic methods that visualization programs use to guess where bonds should be. Indeed. It's a case of the visualization programs doing what you want for simple usage, which is less suited for more complex usage. Given the complexity of learning to use such programs, it seems few people remember the caveats in the documentation about the generation of bonds, or stop to wonder where they come from :-) It's also no wonder that many research groups who do MD use the simulation package most familiar to the leader (from their own doctoral days?), rather than the package best suited in the abstract to the task at hand, since the former strategy makes the best use of the accumulated wisdom of the senior researchers. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
