[gmx-users] Forcefield conversion script for POPC lipids
Hi users, I've searched the web for tools that convert atom names in pdb files from e.g. gromos nomenclature to amber or stockholm lipid nomenclature, but with no luck. Manually mapping the atom names is obviously error prone, so if anyone know of a script or a smart approach for this, do tell. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ -- 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] Forcefield conversion script for POPC lipids
Hi Erik, It's not a very smart approach, but I have a very basic script that can convert CHARMM36 (and probably Slipids as I think they are named and ordered the same) into some united-atom force fields (43A1-S3, Berger, 53A6L and CKP). I can dig it out and send it to you off list, if you are interested? Cheers Tom On 02/06/2014 03:07 PM, Erik Marklund wrote: Hi users, I've searched the web for tools that convert atom names in pdb files from e.g. gromos nomenclature to amber or stockholm lipid nomenclature, but with no luck. Manually mapping the atom names is obviously error prone, so if anyone know of a script or a smart approach for this, do tell. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ -- Dr Thomas Piggot University of Southampton, UK. -- 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] Forcefield conversion script for POPC lipids
Hi Tom, Yes. that sounds like a good starting point. Please send. Erik On 6 Feb 2014, at 19:39, Thomas Piggot t.pig...@soton.ac.uk wrote: Hi Erik, It's not a very smart approach, but I have a very basic script that can convert CHARMM36 (and probably Slipids as I think they are named and ordered the same) into some united-atom force fields (43A1-S3, Berger, 53A6L and CKP). I can dig it out and send it to you off list, if you are interested? Cheers Tom On 02/06/2014 03:07 PM, Erik Marklund wrote: Hi users, I've searched the web for tools that convert atom names in pdb files from e.g. gromos nomenclature to amber or stockholm lipid nomenclature, but with no luck. Manually mapping the atom names is obviously error prone, so if anyone know of a script or a smart approach for this, do tell. Kind regards, Erik Erik Marklund, PhD Postdoctoral Research Associate Department of Chemistry Physical Theoretical Chemistry Laboratory University of Oxford South Parks Road Oxford OX1 3QZ -- Dr Thomas Piggot University of Southampton, UK. -- 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.