[gmx-users] pdb2gmx for small molecules?
Hi, I'm not clear on how to use pdb2gmx to set up a small molecule for simulation, or perhaps the limitations on this capability. My understanding from the latest documentation and the 2013 publication is that v4.5 is capable of handling non-protein/nucleic acid as input. I have created a pdb file for my molecule of interest, but when I invoke pdb2gmx as follows: pdb2gmx -f BrMT_mono_nores.pdb -water tip4 I get a Fatal error message because there is no residue name (it's neither protein or nucleic acid): --- Program pdb2gmx, VERSION 4.5.4 Source code file: /Users/wgallin/Desktop/gromacs-4.5.4/src/kernel/resall.c, line: 581 Fatal error: Residue '' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- and just above that message there is also a Warning in the message saying: Warning: Starting residue 1 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully Is there some documentation that specifically addresses the methods and issues with using pdb2gmx for non-protein/nucleic acid molecules? Thanks. Warren Gallin-- 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] pdb2gmx for small molecules?
On 4/18/13 3:32 PM, Warren Gallin wrote: Hi, I'm not clear on how to use pdb2gmx to set up a small molecule for simulation, or perhaps the limitations on this capability. My understanding from the latest documentation and the 2013 publication is that v4.5 is capable of handling non-protein/nucleic acid as input. I have created a pdb file for my molecule of interest, but when I invoke pdb2gmx as follows: pdb2gmx -f BrMT_mono_nores.pdb -water tip4 I get a Fatal error message because there is no residue name (it's neither protein or nucleic acid): --- Program pdb2gmx, VERSION 4.5.4 Source code file: /Users/wgallin/Desktop/gromacs-4.5.4/src/kernel/resall.c, line: 581 Fatal error: Residue '' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- and just above that message there is also a Warning in the message saying: Warning: Starting residue 1 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully Is there some documentation that specifically addresses the methods and issues with using pdb2gmx for non-protein/nucleic acid molecules? pdb2gmx only knows how to handle what it knows about. There is no generic support for arbitrary compounds. http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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
Re: [gmx-users] pdb2gmx for small molecules?
On 2013-04-18 21:35, Justin Lemkul wrote: On 4/18/13 3:32 PM, Warren Gallin wrote: Hi, I'm not clear on how to use pdb2gmx to set up a small molecule for simulation, or perhaps the limitations on this capability. My understanding from the latest documentation and the 2013 publication is that v4.5 is capable of handling non-protein/nucleic acid as input. I have created a pdb file for my molecule of interest, but when I invoke pdb2gmx as follows: pdb2gmx -f BrMT_mono_nores.pdb -water tip4 I get a Fatal error message because there is no residue name (it's neither protein or nucleic acid): --- Program pdb2gmx, VERSION 4.5.4 Source code file: /Users/wgallin/Desktop/gromacs-4.5.4/src/kernel/resall.c, line: 581 Fatal error: Residue '' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- and just above that message there is also a Warning in the message saying: Warning: Starting residue 1 in chain not identified as Protein/RNA/DNA. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 8 out of 8 lines of specbond.dat converted successfully Is there some documentation that specifically addresses the methods and issues with using pdb2gmx for non-protein/nucleic acid molecules? pdb2gmx only knows how to handle what it knows about. There is no generic support for arbitrary compounds. http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field -Justin Try GAFF using the Ambertools and acpype. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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
