[gmx-users] parameterization of ligand
Hello I have received a parameter of a ligand of a protein from the author of an earlier published work.The parameter is in param.dat format based on ff43a1 force field. Can anybody plz suggest how and where do I put the parameter file in the gromacs.I am using gromacs 4.0 version. Regards Subarna Looking for local information? Find it on Yahoo! Local http://in.local.yahoo.com/___ 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] parameterization of ligand
subarna thakur wrote: Hello I have received a parameter of a ligand of a protein from the author of an earlier published work.The parameter is in param.dat format based on ff43a1 force field. Can anybody plz suggest how and where do I put the parameter file in the gromacs.I am using gromacs 4.0 version. Chapter 5 of the manual is dedicated to topology format and organization. -Justin Regards Subarna Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8 http://in.rd.yahoo.com/tagline_ie8_1/*http://downloads.yahoo.com/in/internetexplorer/. ___ 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 -- 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] Carbohydrate MD Simulation
On Fri, Jul 31, 2009 at 5:19:19 PM, Nancy nancy5vi...@gmail.com wrote: If it necessary to manually create force field parameters for each molecule, then how can one run a simulation involving a number of arbitrary molecules (e.g. a set of mono and disaccharides) for which there are no existing force fields? Do you know of any other MD software package that is capable of running simulations on arbitrary molecules without having to piece together a force field for each molecule? Provided that the desired force field has suitable parameters for a particular bonding situation already, there are software packages that can generate a potentially suitable topology from a molecule's structure. For gromacs topologies, user contributions to gromacs include topolbuild 1.2.1 that supports amber, gaff, glycam, Tripos, and gromacs force fields (my upcoming version 1.3 will also do OPLS-AA with the numeric opls atom types), and topolgen 1.1, a Perl script that supports OPLS-AA. Also available in user contributions is ambconv that takes the file generated by antechamber and leap from amber tools and generates a gromacs topology that uses the amber or gaff forcefield selected when leap was applied to the antechamber output. Another option is the Perl script mktop at http://labmm.iq.ufrj.br/mktop/, documented in Ribeiro, A.A.S.T., Horta, B.A.C., and de Alencastro, R.B. J. Braz. Chem. Soc., Vol. 19, No. 7, 1433-1435, 2008. Also there is acpypi, the AnteChamber Python Parser Interface available at http://code.google.com/p/acpypi/. I hope one of these with careful selection of the force field will be helpful to you. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 ___ 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] Carbohydrate MD Simulation
Hello, I downloaded topolbuild1_2_1.tgz from the URL: http://www.gromacs.org/@api/deki/files/40/=topolbuild1_2_1.tgz However, when I tried to decompress the file, I received the following error message: # tar -xvf topolbuild1_2_1.tgz tar: This does not look like a tar archive tar: Skipping to next header tar: Archive contains obsolescent base-64 headers tar: Error exit delayed from previous errors I also tried to obtain topolbuild 1.2.1 from http://oldwww.gromacs.org/component/option,com_docman/task,doc_download/gid,111/Itemid,26/ but that did not work either. Please advise. Thank you. Nancy On Sat, Aug 1, 2009 at 11:31 AM, Bruce D. Ray bruced...@yahoo.com wrote: On Fri, Jul 31, 2009 at 5:19:19 PM, Nancy nancy5vi...@gmail.com wrote: If it necessary to manually create force field parameters for each molecule, then how can one run a simulation involving a number of arbitrary molecules (e.g. a set of mono and disaccharides) for which there are no existing force fields? Do you know of any other MD software package that is capable of running simulations on arbitrary molecules without having to piece together a force field for each molecule? Provided that the desired force field has suitable parameters for a particular bonding situation already, there are software packages that can generate a potentially suitable topology from a molecule's structure. For gromacs topologies, user contributions to gromacs include topolbuild 1.2.1 that supports amber, gaff, glycam, Tripos, and gromacs force fields (my upcoming version 1.3 will also do OPLS-AA with the numeric opls atom types), and topolgen 1.1, a Perl script that supports OPLS-AA. Also available in user contributions is ambconv that takes the file generated by antechamber and leap from amber tools and generates a gromacs topology that uses the amber or gaff forcefield selected when leap was applied to the antechamber output. Another option is the Perl script mktop at http://labmm.iq.ufrj.br/mktop/, documented in Ribeiro, A.A.S.T., Horta, B.A.C., and de Alencastro, R.B. J. Braz. Chem. Soc., Vol. 19, No. 7, 1433-1435, 2008. Also there is acpypi, the AnteChamber Python Parser Interface available at http://code.google.com/p/acpypi/.* http://code.google.com/p/acpypi/* I hope one of these with careful selection of the force field will be helpful to you. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 ___ 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
Re: [gmx-users] Carbohydrate MD Simulation
Nancy wrote: Hello, I downloaded topolbuild1_2_1.tgz from the URL: http://www.gromacs.org/@api/deki/files/40/=topolbuild1_2_1.tgz However, when I tried to decompress the file, I received the following error message: # tar -xvf topolbuild1_2_1.tgz You have to unzip it as well, i.e.: tar -zxvf topolguild1_2_1.tgz -Justin tar: This does not look like a tar archive tar: Skipping to next header tar: Archive contains obsolescent base-64 headers tar: Error exit delayed from previous errors I also tried to obtain topolbuild 1.2.1 from http://oldwww.gromacs.org/component/option,com_docman/task,doc_download/gid,111/Itemid,26/ but that did not work either. Please advise. Thank you. Nancy On Sat, Aug 1, 2009 at 11:31 AM, Bruce D. Ray bruced...@yahoo.com mailto:bruced...@yahoo.com wrote: On Fri, Jul 31, 2009 at 5:19:19 PM, Nancy nancy5vi...@gmail.com mailto:nancy5vi...@gmail.com wrote: If it necessary to manually create force field parameters for each molecule, then how can one run a simulation involving a number of arbitrary molecules (e.g. a set of mono and disaccharides) for which there are no existing force fields? Do you know of any other MD software package that is capable of running simulations on arbitrary molecules without having to piece together a force field for each molecule? Provided that the desired force field has suitable parameters for a particular bonding situation already, there are software packages that can generate a potentially suitable topology from a molecule's structure. For gromacs topologies, user contributions to gromacs include topolbuild 1.2.1 that supports amber, gaff, glycam, Tripos, and gromacs force fields (my upcoming version 1.3 will also do OPLS-AA with the numeric opls atom types), and topolgen 1.1, a Perl script that supports OPLS-AA. Also available in user contributions is ambconv that takes the file generated by antechamber and leap from amber tools and generates a gromacs topology that uses the amber or gaff forcefield selected when leap was applied to the antechamber output. Another option is the Perl script mktop at http://labmm.iq.ufrj.br/mktop/, documented in Ribeiro, A.A.S.T., Horta, B.A.C., and de Alencastro, R.B. J. Braz. Chem. Soc., Vol. 19, No. 7, 1433-1435, 2008. Also there is acpypi, the AnteChamber Python Parser Interface available at http://code.google.com/p/acpypi/./ http://code.google.com/p/acpypi// I hope one of these with careful selection of the force field will be helpful to you. Sincerely, -- Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto: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 -- 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
[gmx-users] topolbuild1_2_1.tgz decompressing problem
Hello, I downloaded topolbuild1_2_1.tgz from the URL: http://www.gromacs.org/@api/deki/files/40/=topolbuild1_2_1.tgz However, when I tried to decompress the file, I received the following error message: # tar -xvf topolbuild1_2_1.tgz tar: This does not look like a tar archive tar: Skipping to next header tar: Archive contains obsolescent base-64 headers tar: Error exit delayed from previous errors I also tried to obtain topolbuild 1.2.1 from http://oldwww.gromacs.org/component/option,com_docman/task,doc_download/gid,111/Itemid,26/ but that did not work either. Please advise. Thank you. Nancy ___ 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] Carbohydrate MD Simulation
I used gzip to uncompress the file first: # gzip -d topolbuild1_2_1.tgz and then I used tar: # tar -xvf topolbuild1_2_1.tar This seems to work. On Sat, Aug 1, 2009 at 6:05 PM, Justin A. Lemkul jalem...@vt.edu wrote: Nancy wrote: Hello, I downloaded topolbuild1_2_1.tgz from the URL: http://www.gromacs.org/@api/deki/files/40/=topolbuild1_2_1.tgz However, when I tried to decompress the file, I received the following error message: # tar -xvf topolbuild1_2_1.tgz You have to unzip it as well, i.e.: tar -zxvf topolguild1_2_1.tgz -Justin tar: This does not look like a tar archive tar: Skipping to next header tar: Archive contains obsolescent base-64 headers tar: Error exit delayed from previous errors I also tried to obtain topolbuild 1.2.1 from http://oldwww.gromacs.org/component/option,com_docman/task,doc_download/gid,111/Itemid,26/ but that did not work either. Please advise. Thank you. Nancy On Sat, Aug 1, 2009 at 11:31 AM, Bruce D. Ray bruced...@yahoo.commailto: bruced...@yahoo.com wrote: On Fri, Jul 31, 2009 at 5:19:19 PM, Nancy nancy5vi...@gmail.com mailto:nancy5vi...@gmail.com wrote: If it necessary to manually create force field parameters for each molecule, then how can one run a simulation involving a number of arbitrary molecules (e.g. a set of mono and disaccharides) for which there are no existing force fields? Do you know of any other MD software package that is capable of running simulations on arbitrary molecules without having to piece together a force field for each molecule? Provided that the desired force field has suitable parameters for a particular bonding situation already, there are software packages that can generate a potentially suitable topology from a molecule's structure. For gromacs topologies, user contributions to gromacs include topolbuild 1.2.1 that supports amber, gaff, glycam, Tripos, and gromacs force fields (my upcoming version 1.3 will also do OPLS-AA with the numeric opls atom types), and topolgen 1.1, a Perl script that supports OPLS-AA. Also available in user contributions is ambconv that takes the file generated by antechamber and leap from amber tools and generates a gromacs topology that uses the amber or gaff forcefield selected when leap was applied to the antechamber output. Another option is the Perl script mktop at http://labmm.iq.ufrj.br/mktop/, documented in Ribeiro, A.A.S.T., Horta, B.A.C., and de Alencastro, R.B. J. Braz. Chem. Soc., Vol. 19, No. 7, 1433-1435, 2008. Also there is acpypi, the AnteChamber Python Parser Interface available at http://code.google.com/p/acpypi/./ http://code.google.com/p/acpypi/ / I hope one of these with careful selection of the force field will be helpful to you. Sincerely, --Bruce D. Ray, Ph.D. Associate Scientist IUPUI Physics Dept. 402 N. Blackford St. Indianapolis, IN 46202-3273 ___ gmx-users mailing listgmx-users@gromacs.org mailto:gmx-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 mailto: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 -- 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 ___ gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at
