Re: [gmx-users] OPLS-AA topologies for ATP/ADP.
Sorry realised I posted the amber ATP link wrong, it is without the ) at the end: http://www.pharmacy.manchester.ac.uk/bryce/amber Tom --On Thursday, February 26, 2009 17:15:22 + TJ Piggot wrote: Some of these charges look a bit suspect to me (eg the charge on the gamma phosphate). If you do not need to use OPLS then there is ATP included in the (united atom) gromos forcefields (see the top folder) and also ATP parameters available for the (all atom) Amber forcefields (see http://www.pharmacy.manchester.ac.uk/bryce/amber), all you have to do is convert them into a gromacs format Tom --On Thursday, February 26, 2009 08:33:06 -0800 "Bruce D. Ray" wrote: On Wednesday, February 25, 2009 12:06:20 AM, Lucio Ricardo Montero Valenzuela wrote: Does anybody have the topology files for ATP and/or ADP for the OPLS-AA forcefield?. If not, how can I parameterize this molecules?. Best regards. Lucio Montero. Lucio Ricardo Montero Valenzuela Instituto de Biotecnologia, UNAM Departamento de Biologia Molecular de Plantas Av. Universidad 2001, Col. Chamilpa Cuernavaca 62210 Mexico I've not tested this at all, but from my attempts to add OPLS-AA to topolbuild, I get the following that might be suitable for insertion in the oplsaa rtp: [ ATP ] [ atoms ] O9Popls_441 -0.635 0 ;O2 O8Popls_441 -0.635 1 ;O2 O7Popls_441 -0.635 2 ;O2 PGopls_445 0.072 3 ;P O6Popls_442 -0.286 4 ;OS O5Popls_441 -0.516 5 ;O2 O4Popls_441 -0.516 6 ;O2 PBopls_440 0.280 7 ;P O3Popls_442 -0.250 8 ;OS O2Popls_441 -0.516 9 ;O2 O1Popls_441 -0.51610 ;O2 PAopls_440 0.27611 ;P O5*opls_442 -0.31512 ;OS C5*opls_443 0.08513 ;CT H5*1opls_444 0.05914 ;HC H5*2opls_444 0.05915 ;HC C4*opls_174 0.11316 ;CT H4*opls_176 0.06517 ;HC O4*opls_186 -0.34818 ;OS C1*opls_193 0.16019 ;CO H1*opls_194 0.08420 ;HC N9opls_354B -0.24521 ;NA C8opls_353 0.09222 ;CK H8opls_359 0.10023 ;H5 N7opls_352 -0.23324 ;NB C5opls_350 0.14525 ;CB C6opls_351 0.14726 ;CA N6opls_356 -0.34127 ;N2 H61opls_357 0.14428 ;H H62opls_358 0.14429 ;H N1opls_346 -0.21930 ;NC C2opls_347 0.12031 ;CQ H2opls_355 0.06632 ;H5 N3opls_348 -0.21833 ;NC C4opls_349 0.15934 ;CB C2*opls_174 0.12735 ;CT H2*opls_176 0.10036 ;HC O2'opls_171 -0.38537 ;OH H2'opls_172 0.21038 ;HO C3*opls_174 0.11339 ;CT H3*opls_176 0.06540 ;HC O3'opls_171 -0.38641 ;OH H3'opls_172 0.21042 ;HO [ bonds ] PG O9P PG O8P PG O7P O6PPG PB O6P PB O5P PB O4P O3PPB PA O3P PA O2P PA O1P PA O5* O5* C5* C5* C4* C5* H5*1 C5* H5*2 C4* O4* C4* H4* C4* C3* O4* C1* C1*N9 C1* H1* C1* C2* N9C8 C8H8 C8N7 N7C5 C5C6 C5C4 C6N6 N6 H61 N6 H62 C6N1 N1C2 C2H2 C2N3 N3C4 C4N9 C2* C3* C2* H2* C2* O2' O2' H2' C3* H3* C3* O3' O3' H3' Please let me know if this actually works for computations. Charges were derived from the .mol2 file generated by Sybyl. 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://www.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 -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 in
Re: [gmx-users] OPLS-AA topologies for ATP/ADP.
Some of these charges look a bit suspect to me (eg the charge on the gamma phosphate). If you do not need to use OPLS then there is ATP included in the (united atom) gromos forcefields (see the top folder) and also ATP parameters available for the (all atom) Amber forcefields (see http://www.pharmacy.manchester.ac.uk/bryce/amber), all you have to do is convert them into a gromacs format Tom --On Thursday, February 26, 2009 08:33:06 -0800 "Bruce D. Ray" wrote: On Wednesday, February 25, 2009 12:06:20 AM, Lucio Ricardo Montero Valenzuela wrote: Does anybody have the topology files for ATP and/or ADP for the OPLS-AA forcefield?. If not, how can I parameterize this molecules?. Best regards. Lucio Montero. Lucio Ricardo Montero Valenzuela Instituto de Biotecnologia, UNAM Departamento de Biologia Molecular de Plantas Av. Universidad 2001, Col. Chamilpa Cuernavaca 62210 Mexico I've not tested this at all, but from my attempts to add OPLS-AA to topolbuild, I get the following that might be suitable for insertion in the oplsaa rtp: [ ATP ] [ atoms ] O9Popls_441 -0.635 0 ;O2 O8Popls_441 -0.635 1 ;O2 O7Popls_441 -0.635 2 ;O2 PGopls_445 0.072 3 ;P O6Popls_442 -0.286 4 ;OS O5Popls_441 -0.516 5 ;O2 O4Popls_441 -0.516 6 ;O2 PBopls_440 0.280 7 ;P O3Popls_442 -0.250 8 ;OS O2Popls_441 -0.516 9 ;O2 O1Popls_441 -0.51610 ;O2 PAopls_440 0.27611 ;P O5*opls_442 -0.31512 ;OS C5*opls_443 0.08513 ;CT H5*1opls_444 0.05914 ;HC H5*2opls_444 0.05915 ;HC C4*opls_174 0.11316 ;CT H4*opls_176 0.06517 ;HC O4*opls_186 -0.34818 ;OS C1*opls_193 0.16019 ;CO H1*opls_194 0.08420 ;HC N9opls_354B -0.24521 ;NA C8opls_353 0.09222 ;CK H8opls_359 0.10023 ;H5 N7opls_352 -0.23324 ;NB C5opls_350 0.14525 ;CB C6opls_351 0.14726 ;CA N6opls_356 -0.34127 ;N2 H61opls_357 0.14428 ;H H62opls_358 0.14429 ;H N1opls_346 -0.21930 ;NC C2opls_347 0.12031 ;CQ H2opls_355 0.06632 ;H5 N3opls_348 -0.21833 ;NC C4opls_349 0.15934 ;CB C2*opls_174 0.12735 ;CT H2*opls_176 0.10036 ;HC O2'opls_171 -0.38537 ;OH H2'opls_172 0.21038 ;HO C3*opls_174 0.11339 ;CT H3*opls_176 0.06540 ;HC O3'opls_171 -0.38641 ;OH H3'opls_172 0.21042 ;HO [ bonds ] PG O9P PG O8P PG O7P O6PPG PB O6P PB O5P PB O4P O3PPB PA O3P PA O2P PA O1P PA O5* O5* C5* C5* C4* C5* H5*1 C5* H5*2 C4* O4* C4* H4* C4* C3* O4* C1* C1*N9 C1* H1* C1* C2* N9C8 C8H8 C8N7 N7C5 C5C6 C5C4 C6N6 N6 H61 N6 H62 C6N1 N1C2 C2H2 C2N3 N3C4 C4N9 C2* C3* C2* H2* C2* O2' O2' H2' C3* H3* C3* O3' O3' H3' Please let me know if this actually works for computations. Charges were derived from the .mol2 file generated by Sybyl. 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://www.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 -- TJ Piggot t.pig...@bristol.ac.uk University of Bristol, UK. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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] OPLS-AA topologies for ATP/ADP.
On Wednesday, February 25, 2009 12:06:20 AM, Lucio Ricardo Montero Valenzuela wrote: > Does anybody have the topology files for ATP and/or ADP for the OPLS-AA > forcefield?. If not, how can I parameterize this molecules?. > Best regards. >Lucio Montero. > > Lucio Ricardo Montero Valenzuela > Instituto de Biotecnologia, UNAM > Departamento de Biologia Molecular de Plantas > Av. Universidad 2001, Col. Chamilpa > Cuernavaca 62210 > Mexico I've not tested this at all, but from my attempts to add OPLS-AA to topolbuild, I get the following that might be suitable for insertion in the oplsaa rtp: [ ATP ] [ atoms ] O9Popls_441 -0.635 0 ;O2 O8Popls_441 -0.635 1 ;O2 O7Popls_441 -0.635 2 ;O2 PGopls_445 0.072 3 ;P O6Popls_442 -0.286 4 ;OS O5Popls_441 -0.516 5 ;O2 O4Popls_441 -0.516 6 ;O2 PBopls_440 0.280 7 ;P O3Popls_442 -0.250 8 ;OS O2Popls_441 -0.516 9 ;O2 O1Popls_441 -0.51610 ;O2 PAopls_440 0.27611 ;P O5*opls_442 -0.31512 ;OS C5*opls_443 0.08513 ;CT H5*1opls_444 0.05914 ;HC H5*2opls_444 0.05915 ;HC C4*opls_174 0.11316 ;CT H4*opls_176 0.06517 ;HC O4*opls_186 -0.34818 ;OS C1*opls_193 0.16019 ;CO H1*opls_194 0.08420 ;HC N9opls_354B -0.24521 ;NA C8opls_353 0.09222 ;CK H8opls_359 0.10023 ;H5 N7opls_352 -0.23324 ;NB C5opls_350 0.14525 ;CB C6opls_351 0.14726 ;CA N6opls_356 -0.34127 ;N2 H61opls_357 0.14428 ;H H62opls_358 0.14429 ;H N1opls_346 -0.21930 ;NC C2opls_347 0.12031 ;CQ H2opls_355 0.06632 ;H5 N3opls_348 -0.21833 ;NC C4opls_349 0.15934 ;CB C2*opls_174 0.12735 ;CT H2*opls_176 0.10036 ;HC O2'opls_171 -0.38537 ;OH H2'opls_172 0.21038 ;HO C3*opls_174 0.11339 ;CT H3*opls_176 0.06540 ;HC O3'opls_171 -0.38641 ;OH H3'opls_172 0.21042 ;HO [ bonds ] PG O9P PG O8P PG O7P O6PPG PB O6P PB O5P PB O4P O3PPB PA O3P PA O2P PA O1P PA O5* O5* C5* C5* C4* C5* H5*1 C5* H5*2 C4* O4* C4* H4* C4* C3* O4* C1* C1*N9 C1* H1* C1* C2* N9C8 C8H8 C8N7 N7C5 C5C6 C5C4 C6N6 N6 H61 N6 H62 C6N1 N1C2 C2H2 C2N3 N3C4 C4N9 C2* C3* C2* H2* C2* O2' O2' H2' C3* H3* C3* O3' O3' H3' Please let me know if this actually works for computations. Charges were derived from the .mol2 file generated by Sybyl. 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://www.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] OPLS-AA topologies for ATP/ADP.
Thanks very much. Lucio Montero. -- From: "Justin A. Lemkul" Sent: Wednesday, February 25, 2009 5:55 AM To: "Discusson list for GROMACS users" Subject: Re: [gmx-users] OPLS-AA topologies for ATP/ADP. Lucio Ricardo Montero Valenzuela wrote: Does anybody have the topology files for ATP and/or ADP for the OPLS-AA forcefield?. If not, how can I parameterize this molecules?. Methods for parameterization can be found in the primary literature for the force field. A few notes on this advanced topic: http://wiki.gromacs.org/index.php/Parameterization -Justin Best regards. Lucio Montero. Lucio Ricardo Montero Valenzuela Instituto de Biotecnologia, UNAM Departamento de Biologia Molecular de Plantas Av. Universidad 2001, Col. Chamilpa Cuernavaca 62210 Mexico Este mensaje fue enviado desde el servidor Webmail del Instituto de Biotecnologia. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 Graduate Research Assistant 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://www.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://www.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] OPLS-AA topologies for ATP/ADP.
Lucio Ricardo Montero Valenzuela wrote: Does anybody have the topology files for ATP and/or ADP for the OPLS-AA forcefield?. If not, how can I parameterize this molecules?. Methods for parameterization can be found in the primary literature for the force field. A few notes on this advanced topic: http://wiki.gromacs.org/index.php/Parameterization -Justin Best regards. Lucio Montero. Lucio Ricardo Montero Valenzuela Instituto de Biotecnologia, UNAM Departamento de Biologia Molecular de Plantas Av. Universidad 2001, Col. Chamilpa Cuernavaca 62210 Mexico Este mensaje fue enviado desde el servidor Webmail del Instituto de Biotecnologia. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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 Graduate Research Assistant 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://www.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] OPLS-AA topologies for ATP/ADP.
Does anybody have the topology files for ATP and/or ADP for the OPLS-AA forcefield?. If not, how can I parameterize this molecules?. Best regards. Lucio Montero. Lucio Ricardo Montero Valenzuela Instituto de Biotecnologia, UNAM Departamento de Biologia Molecular de Plantas Av. Universidad 2001, Col. Chamilpa Cuernavaca 62210 Mexico Este mensaje fue enviado desde el servidor Webmail del Instituto de Biotecnologia. ___ gmx-users mailing listgmx-users@gromacs.org http://www.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
