Re: [gmx-users] pdb generator
Hello Momin The best tool I have found for dealing with cif files, including exporting to pdb, is Mercury. You can download it for free from: https://www.ccdc.cam.ac.uk/Community/csd-community/freemercury/ Hope this helps Victor El mar., 13 nov. 2018 a las 8:04, Momin Ahmad () escribió: > Hi, > > is there a tool where i can use for example a .cif file (or .xyz) file > to generate a .pdb file with correct classification? For example > Avogadro classifies all atoms as LIG and i cannot change it. Is there > also another tool which can be used to generate large scale crystal > structures with building blocks as input? > > > Cheers > > Momin > > -- > Momin Ahmad > > Karlsruhe Institute of Technology (KIT) > Steinbuch Centre for Computing (SCC) > Hermann-von-Helmholtz-Platz 1 > 76344 Eggenstein-Leopoldshafen > Phone: +49 721 608-24286 > E-Mail: momin.ah...@kit.edu > > -- > 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] pdb generator
You should know how many atoms in each residue then how many residues of XXX you have then you can see. Suggestion, if possible use sperate pdb files then use solvation option to produce your system .gro or pdb. This will help you in editing each pdb then get your correct gromacs input files. Best On Tue, Nov 13, 2018 at 9:35 AM Momin Ahmad wrote: > Hi Ali, > > thanks for you help. How can you distinguish between a C atom from > residue XXX and another C atom from residue YYY when there are about > 2000 atoms in the file. Did you write a script for that? If there doesnt > exist a tool with a GUI to solve this then i will have to write my own > builder. > > Cheers > > Momin > > Am 13.11.18 um 16:31 schrieb Ali Ahmed: > > well if you use Linux then you can use GVim to do highlight and do simple > > changes on one type only then use find and replace option. That what I do > > when I have more than one type. It needs one hour practice then you will > be > > ok. Or you can write a script for such things. > > Best > > > > On Tue, Nov 13, 2018 at 9:15 AM Momin Ahmad wrote: > > > >> Hi Ali, > >> > >> my problem is that there is not only one molecule but two different > >> molecules which build up a crystaline structure. For example i have 10 > >> XXX and 100 YYY in the .pdb file. > >> > >> Cheers > >> > >> Momin > >> > >> Am 13.11.18 um 16:12 schrieb Ali Ahmed: > >>> Hi, > >>> I use Avogadro and it is easy to change LIG to anything you want. I > just > >>> use find and replace option which takes less than a minute. > >>> Best > >>> Ali > >>> > >>> On Tue, Nov 13, 2018 at 8:04 AM Momin Ahmad > wrote: > >>> > Hi, > > is there a tool where i can use for example a .cif file (or .xyz) file > to generate a .pdb file with correct classification? For example > Avogadro classifies all atoms as LIG and i cannot change it. Is there > also another tool which can be used to generate large scale crystal > structures with building blocks as input? > > > Cheers > > Momin > > -- > Momin Ahmad > > Karlsruhe Institute of Technology (KIT) > Steinbuch Centre for Computing (SCC) > Hermann-von-Helmholtz-Platz 1 > 76344 Eggenstein-Leopoldshafen > Phone: +49 721 608-24286 > E-Mail: momin.ah...@kit.edu > > -- > 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. > > >> -- > >> Momin Ahmad > >> > >> Karlsruhe Institute of Technology (KIT) > >> Steinbuch Centre for Computing (SCC) > >> Hermann-von-Helmholtz-Platz 1 > >> 76344 Eggenstein-Leopoldshafen > >> Phone: +49 721 608-24286 > >> E-Mail: momin.ah...@kit.edu > >> > >> -- > >> 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. > >> > -- > Momin Ahmad > > Karlsruhe Institute of Technology (KIT) > Steinbuch Centre for Computing (SCC) > Hermann-von-Helmholtz-Platz 1 > 76344 Eggenstein-Leopoldshafen > Phone: +49 721 608-24286 > E-Mail: momin.ah...@kit.edu > > -- > 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] pdb generator
Hi Ali, thanks for you help. How can you distinguish between a C atom from residue XXX and another C atom from residue YYY when there are about 2000 atoms in the file. Did you write a script for that? If there doesnt exist a tool with a GUI to solve this then i will have to write my own builder. Cheers Momin Am 13.11.18 um 16:31 schrieb Ali Ahmed: well if you use Linux then you can use GVim to do highlight and do simple changes on one type only then use find and replace option. That what I do when I have more than one type. It needs one hour practice then you will be ok. Or you can write a script for such things. Best On Tue, Nov 13, 2018 at 9:15 AM Momin Ahmad wrote: Hi Ali, my problem is that there is not only one molecule but two different molecules which build up a crystaline structure. For example i have 10 XXX and 100 YYY in the .pdb file. Cheers Momin Am 13.11.18 um 16:12 schrieb Ali Ahmed: Hi, I use Avogadro and it is easy to change LIG to anything you want. I just use find and replace option which takes less than a minute. Best Ali On Tue, Nov 13, 2018 at 8:04 AM Momin Ahmad wrote: Hi, is there a tool where i can use for example a .cif file (or .xyz) file to generate a .pdb file with correct classification? For example Avogadro classifies all atoms as LIG and i cannot change it. Is there also another tool which can be used to generate large scale crystal structures with building blocks as input? Cheers Momin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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. -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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. -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] pdb generator
well if you use Linux then you can use GVim to do highlight and do simple changes on one type only then use find and replace option. That what I do when I have more than one type. It needs one hour practice then you will be ok. Or you can write a script for such things. Best On Tue, Nov 13, 2018 at 9:15 AM Momin Ahmad wrote: > Hi Ali, > > my problem is that there is not only one molecule but two different > molecules which build up a crystaline structure. For example i have 10 > XXX and 100 YYY in the .pdb file. > > Cheers > > Momin > > Am 13.11.18 um 16:12 schrieb Ali Ahmed: > > Hi, > > I use Avogadro and it is easy to change LIG to anything you want. I just > > use find and replace option which takes less than a minute. > > Best > > Ali > > > > On Tue, Nov 13, 2018 at 8:04 AM Momin Ahmad wrote: > > > >> Hi, > >> > >> is there a tool where i can use for example a .cif file (or .xyz) file > >> to generate a .pdb file with correct classification? For example > >> Avogadro classifies all atoms as LIG and i cannot change it. Is there > >> also another tool which can be used to generate large scale crystal > >> structures with building blocks as input? > >> > >> > >> Cheers > >> > >> Momin > >> > >> -- > >> Momin Ahmad > >> > >> Karlsruhe Institute of Technology (KIT) > >> Steinbuch Centre for Computing (SCC) > >> Hermann-von-Helmholtz-Platz 1 > >> 76344 Eggenstein-Leopoldshafen > >> Phone: +49 721 608-24286 > >> E-Mail: momin.ah...@kit.edu > >> > >> -- > >> 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. > >> > -- > Momin Ahmad > > Karlsruhe Institute of Technology (KIT) > Steinbuch Centre for Computing (SCC) > Hermann-von-Helmholtz-Platz 1 > 76344 Eggenstein-Leopoldshafen > Phone: +49 721 608-24286 > E-Mail: momin.ah...@kit.edu > > -- > 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] pdb generator
Hi Ali, my problem is that there is not only one molecule but two different molecules which build up a crystaline structure. For example i have 10 XXX and 100 YYY in the .pdb file. Cheers Momin Am 13.11.18 um 16:12 schrieb Ali Ahmed: Hi, I use Avogadro and it is easy to change LIG to anything you want. I just use find and replace option which takes less than a minute. Best Ali On Tue, Nov 13, 2018 at 8:04 AM Momin Ahmad wrote: Hi, is there a tool where i can use for example a .cif file (or .xyz) file to generate a .pdb file with correct classification? For example Avogadro classifies all atoms as LIG and i cannot change it. Is there also another tool which can be used to generate large scale crystal structures with building blocks as input? Cheers Momin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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. -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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] pdb generator
Hi, I use Avogadro and it is easy to change LIG to anything you want. I just use find and replace option which takes less than a minute. Best Ali On Tue, Nov 13, 2018 at 8:04 AM Momin Ahmad wrote: > Hi, > > is there a tool where i can use for example a .cif file (or .xyz) file > to generate a .pdb file with correct classification? For example > Avogadro classifies all atoms as LIG and i cannot change it. Is there > also another tool which can be used to generate large scale crystal > structures with building blocks as input? > > > Cheers > > Momin > > -- > Momin Ahmad > > Karlsruhe Institute of Technology (KIT) > Steinbuch Centre for Computing (SCC) > Hermann-von-Helmholtz-Platz 1 > 76344 Eggenstein-Leopoldshafen > Phone: +49 721 608-24286 > E-Mail: momin.ah...@kit.edu > > -- > 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.
[gmx-users] pdb generator
Hi, is there a tool where i can use for example a .cif file (or .xyz) file to generate a .pdb file with correct classification? For example Avogadro classifies all atoms as LIG and i cannot change it. Is there also another tool which can be used to generate large scale crystal structures with building blocks as input? Cheers Momin -- Momin Ahmad Karlsruhe Institute of Technology (KIT) Steinbuch Centre for Computing (SCC) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Phone: +49 721 608-24286 E-Mail: momin.ah...@kit.edu -- 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.
