Re: [gmx-users] OPLS-AA topologies for ATP
Well I would suggest you should do some very careful testing to validate the combination of CHARMM charges and one dihedral with the rest of the parameters from OPLS. It is not very common (or generally wise) to mix and match parameters from different forcefields, see: http://www.gromacs.org/index.php?title=Documentation/How-tos/Parameterization I would also say that you should also take care with the OPLS-AA DNA parameters as these have not been substantially tested/used and so you should double check the atom types for yourself. On the specific topic of ATP for OPLS-AA/L I have performed simulations using the AMBER ATP parameters in OPLS-AA/L (with no changes for anything such as the different combination rules) and have found these parameters perform just as well as with the AMBER forcefields. There will be a section about this (showing the results from some of the tests I performed) in a paper I am currently writing. The AMBER ATP parameters can be found at: http://www.pharmacy.manchester.ac.uk/bryce/amber#cof However, I would also ask is there a specific reason you wish to use OPLS-AA/L? If not then it is probably easier to use one of the AMBER forcefields with these parameters as you do not need to do any testing (or wait for me to publish my work!) Cheers Tom BIN ZHANG wrote: Hi, I recently made up a topology for ADP. You can probably modify it to ATP easily. I used native OPLS atom types based on the DNA parameters (http://rnp-group.genebee.msu.su/3d/ff.htm). The charges are copied from CHARMM27. Also, there is one dihedral angle missing, again, copied from CHARMM. Please let me know if you have any question, suggestion, Cheers, Bin === In the ffoplsaa.rtp file, I added: [ ADP ] [ atoms ] PBopls_440 1.100 0 ;P O1Bopls_441 -0.900 1 ;O O2Bopls_441 -0.900 2 ;O O3Bopls_441 -0.900 3 ;O PAopls_440 1.500 4 ;P O1Aopls_441 -0.820 5 ;O2 O2Aopls_441 -0.820 6 ;O2 O3Aopls_442 -0.740 7 ;OS O5'opls_442 -0.620 8 ;OS C5'opls_443 -0.080 9 ;CT H5''opls_444 0.09010 ;HC H5' opls_444 0.09011 ;HC C4'opls_158 0.16012 ;CT H4'opls_156 0.09013 ;HC O4'opls_180 -0.50014 ;OS C1'opls_158 0.16015 ;CT H1'opls_156 0.09016 ;HC N9opls_354 -0.05017 ;NA C8opls_353 0.34018 ;CK H8opls_359 0.12019 ;H5 N7opls_352 -0.71020 ;NB C5opls_350 0.28021 ;CB C6opls_351 0.46022 ;CA N6opls_356 -0.77023 ;N2 H61opls_357 0.38024 ;H H62opls_358 0.38025 ;H N1opls_346 -0.74026 ;NC C2opls_347 0.50027 ;CQ H2opls_355 0.13028 ;H5 N3opls_348 -0.75029 ;NC C4opls_349 0.43030 ;CB C2'opls_158 0.14031 ;CT H2''opls_156 0.09032 ;HC O2'opls_171 -0.66033 ;OH H2'opls_172 0.43034 ;HO C3'opls_158 0.14035 ;CT H3'opls_156 0.09036 ;HC O3'opls_171 -0.66037 ;OS H3Topls_172 0.43038 [ bonds ] PBO3A PBO1B PBO2B PBO3B O3A PA PAO1A PAO2A PAO5' O3'H3T O5'C5' C5'C4' C4'O4' C4'C3' O4'C1' C1' N9 C1'C2' N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 N6H61 N6H62 C6 C5 C5 N7 C2'C3' C2'O2' O2'H2' C3'O3' C1'H1' C2' H2'' C3'H3' C4'H4' C5'H5' C5' H5'' C8 H8 C2 H2 N1 C6 N3 C2 C4 C5 N7 C8 === === In the ffoplsaabon.itp file, I added: ; copied from ffoplsaanr [ angletypes ] NA CT OS 1 109.500418.680 ; DNA DCY [ dihedraltypes ] ; these are again copied from ffoplsaanr NA C CM CT 3 30.35430 0.0 -30.35430 0.0 0.0 0.0 ; aromatic ring DNA DTH C CM CT HC 3 -0.77874 -2.33623 0.0 3.11498 0.0 0.0 ; aromatic ring DNA DTH HC CT CT NA 3 0.97134 2.91401 0.0 -3.88535 0.0 0.0 ; RNA NA CT CT OH 3 16.74720 -16.74720 0.0 0.0 0.0 0.0 ; RNA CM NA CT OS 3 -3.14010 -3.14010 6.28020 0.0 0.0 0.0 ; DNA DCY C NA CT OS 3 -3.14010 -3.14010 6.28020 0.0 0.0 0.0 ; DNA DCY CT OS CT NA 3 -5.23350 7.32690 6.28020 -8.37360 0.0 0.0 ; [ dihedraltypes ] ; copied from charmm O2 POS P 1 0.0 0.12553.0 O2 POS P 1 0.0 0.41842.0 OS POS P 1 0.0 0.12553.0 OS POS P
Re: [gmx-users] OPLS-AA topologies for ATP
Dear Tom: Thanks for your suggestion. You are absolutely right on doing more testings. I simply haven't figure out what the appropriate test is yet. Could you be more specific about these parameters perform just as well as? What kind of test did you do? Also, is there a reason why you choose Amber over Charmm? Is it more compatible with OPLS? Thanks, Bin On Jun 23, 2010, at 2:48 AM, Thomas Piggot wrote: Well I would suggest you should do some very careful testing to validate the combination of CHARMM charges and one dihedral with the rest of the parameters from OPLS. It is not very common (or generally wise) to mix and match parameters from different forcefields, see: http://www.gromacs.org/index.php?title=Documentation/How-tos/Parameterization I would also say that you should also take care with the OPLS-AA DNA parameters as these have not been substantially tested/used and so you should double check the atom types for yourself. On the specific topic of ATP for OPLS-AA/L I have performed simulations using the AMBER ATP parameters in OPLS-AA/L (with no changes for anything such as the different combination rules) and have found these parameters perform just as well as with the AMBER forcefields. There will be a section about this (showing the results from some of the tests I performed) in a paper I am currently writing. The AMBER ATP parameters can be found at: http://www.pharmacy.manchester.ac.uk/bryce/amber#cof However, I would also ask is there a specific reason you wish to use OPLS-AA/L? If not then it is probably easier to use one of the AMBER forcefields with these parameters as you do not need to do any testing (or wait for me to publish my work!) Cheers Tom BIN ZHANG wrote: Hi, I recently made up a topology for ADP. You can probably modify it to ATP easily. I used native OPLS atom types based on the DNA parameters (http://rnp-group.genebee.msu.su/3d/ff.htm). The charges are copied from CHARMM27. Also, there is one dihedral angle missing, again, copied from CHARMM. Please let me know if you have any question, suggestion, Cheers, Bin === In the ffoplsaa.rtp file, I added: [ ADP ] [ atoms ] PBopls_440 1.100 0 ;P O1Bopls_441 -0.900 1 ;O O2Bopls_441 -0.900 2 ;O O3Bopls_441 -0.900 3 ;O PAopls_440 1.500 4 ;P O1Aopls_441 -0.820 5 ;O2 O2Aopls_441 -0.820 6 ;O2 O3Aopls_442 -0.740 7 ;OS O5'opls_442 -0.620 8 ;OS C5'opls_443 -0.080 9 ;CT H5''opls_444 0.09010 ;HC H5' opls_444 0.09011 ;HC C4'opls_158 0.16012 ;CT H4'opls_156 0.09013 ;HC O4'opls_180 -0.50014 ;OS C1'opls_158 0.16015 ;CT H1'opls_156 0.09016 ;HC N9opls_354 -0.05017 ;NA C8opls_353 0.34018 ;CK H8opls_359 0.12019 ;H5 N7opls_352 -0.71020 ;NB C5opls_350 0.28021 ;CB C6opls_351 0.46022 ;CA N6opls_356 -0.77023 ;N2 H61opls_357 0.38024 ;H H62opls_358 0.38025 ;H N1opls_346 -0.74026 ;NC C2opls_347 0.50027 ;CQ H2opls_355 0.13028 ;H5 N3opls_348 -0.75029 ;NC C4opls_349 0.43030 ;CB C2'opls_158 0.14031 ;CT H2''opls_156 0.09032 ;HC O2'opls_171 -0.66033 ;OH H2'opls_172 0.43034 ;HO C3'opls_158 0.14035 ;CT H3'opls_156 0.09036 ;HC O3'opls_171 -0.66037 ;OS H3Topls_172 0.43038 [ bonds ] PBO3A PBO1B PBO2B PBO3B O3A PA PAO1A PAO2A PAO5' O3'H3T O5'C5' C5'C4' C4'O4' C4'C3' O4'C1' C1' N9 C1'C2' N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 N6H61 N6H62 C6 C5 C5 N7 C2'C3' C2'O2' O2'H2' C3'O3' C1'H1' C2' H2'' C3'H3' C4'H4' C5'H5' C5' H5'' C8 H8 C2 H2 N1 C6 N3 C2 C4 C5 N7 C8 === === In the ffoplsaabon.itp file, I added: ; copied from ffoplsaanr [ angletypes ] NA CT OS 1 109.500418.680 ; DNA DCY [ dihedraltypes ] ; these are again copied from ffoplsaanr NA C CM CT 3 30.35430 0.0 -30.35430 0.0 0.0 0.0 ; aromatic ring DNA DTH C CM CT HC 3 -0.77874 -2.33623 0.0 3.11498 0.0 0.0 ; aromatic ring DNA DTH HC CT CT NA 3 0.97134 2.91401 0.0 -3.88535 0.0 0.0 ; RNA NA CT CT OH 3 16.74720 -16.74720 0.0 0.0 0.0 0.0 ; RNA CM NA CT OS 3 -3.14010 -3.14010 6.28020 0.0 0.0 0.0 ; DNA DCY C NA CT OS 3 -3.14010 -3.14010
Re: [gmx-users] OPLS-AA topologies for ATP
I chose the AMBER ATP for OPLS as I wanted to simulate my system with two different all-atom forcefields and knew that I could use AMBER in GROMACS with these published parameters (through use of the ffamber ports). The only other all-atom forcefield in GROMACS at that time was OPLS and rather than attempt a new parameterisation of ATP for OPLS I first tried these parameters to see how they would perform. For the testing then I am sure if you think about this then you can come up with some idea's of what good tests would be. If not then look for papers where people have done similar things in the past. Again I must reiterate if you wish to simulate ATP with an all-atom forcefield then I would suggest it is currently much easier to use the AMBER forcefields than to use OPLS unless there is a specific reason to use OPLS. Cheers Tom BIN ZHANG wrote: Dear Tom: Thanks for your suggestion. You are absolutely right on doing more testings. I simply haven't figure out what the appropriate test is yet. Could you be more specific about these parameters perform just as well as? What kind of test did you do? Also, is there a reason why you choose Amber over Charmm? Is it more compatible with OPLS? Thanks, Bin On Jun 23, 2010, at 2:48 AM, Thomas Piggot wrote: Well I would suggest you should do some very careful testing to validate the combination of CHARMM charges and one dihedral with the rest of the parameters from OPLS. It is not very common (or generally wise) to mix and match parameters from different forcefields, see: http://www.gromacs.org/index.php?title=Documentation/How-tos/Parameterization I would also say that you should also take care with the OPLS-AA DNA parameters as these have not been substantially tested/used and so you should double check the atom types for yourself. On the specific topic of ATP for OPLS-AA/L I have performed simulations using the AMBER ATP parameters in OPLS-AA/L (with no changes for anything such as the different combination rules) and have found these parameters perform just as well as with the AMBER forcefields. There will be a section about this (showing the results from some of the tests I performed) in a paper I am currently writing. The AMBER ATP parameters can be found at: http://www.pharmacy.manchester.ac.uk/bryce/amber#cof However, I would also ask is there a specific reason you wish to use OPLS-AA/L? If not then it is probably easier to use one of the AMBER forcefields with these parameters as you do not need to do any testing (or wait for me to publish my work!) Cheers Tom BIN ZHANG wrote: Hi, I recently made up a topology for ADP. You can probably modify it to ATP easily. I used native OPLS atom types based on the DNA parameters (http://rnp-group.genebee.msu.su/3d/ff.htm). The charges are copied from CHARMM27. Also, there is one dihedral angle missing, again, copied from CHARMM. Please let me know if you have any question, suggestion, Cheers, Bin === In the ffoplsaa.rtp file, I added: [ ADP ] [ atoms ] PBopls_440 1.100 0 ;P O1Bopls_441 -0.900 1 ;O O2Bopls_441 -0.900 2 ;O O3Bopls_441 -0.900 3 ;O PAopls_440 1.500 4 ;P O1Aopls_441 -0.820 5 ;O2 O2Aopls_441 -0.820 6 ;O2 O3Aopls_442 -0.740 7 ;OS O5'opls_442 -0.620 8 ;OS C5'opls_443 -0.080 9 ;CT H5''opls_444 0.09010 ;HC H5' opls_444 0.09011 ;HC C4'opls_158 0.16012 ;CT H4'opls_156 0.09013 ;HC O4'opls_180 -0.50014 ;OS C1'opls_158 0.16015 ;CT H1'opls_156 0.09016 ;HC N9opls_354 -0.05017 ;NA C8opls_353 0.34018 ;CK H8opls_359 0.12019 ;H5 N7opls_352 -0.71020 ;NB C5opls_350 0.28021 ;CB C6opls_351 0.46022 ;CA N6opls_356 -0.77023 ;N2 H61opls_357 0.38024 ;H H62opls_358 0.38025 ;H N1opls_346 -0.74026 ;NC C2opls_347 0.50027 ;CQ H2opls_355 0.13028 ;H5 N3opls_348 -0.75029 ;NC C4opls_349 0.43030 ;CB C2'opls_158 0.14031 ;CT H2''opls_156 0.09032 ;HC O2'opls_171 -0.66033 ;OH H2'opls_172 0.43034 ;HO C3'opls_158 0.14035 ;CT H3'opls_156 0.09036 ;HC O3'opls_171 -0.66037 ;OS H3Topls_172 0.43038 [ bonds ] PBO3A PBO1B PBO2B PBO3B O3A PA PAO1A PAO2A PAO5' O3'H3T O5'C5' C5'C4' C4'O4' C4'C3' O4'C1' C1' N9 C1'C2' N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 N6H61 N6H62 C6 C5 C5 N7 C2'C3' C2'O2' O2'H2' C3'O3' C1'H1' C2' H2'' C3'H3' C4'H4' C5'H5' C5' H5'' C8 H8 C2 H2 N1 C6 N3 C2 C4 C5 N7 C8 ===
[gmx-users] OPLS-AA topologies for ATP
Hi, Does anyone have OPLS-AA topologies for ATP? Thanks, Efrat-- 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] OPLS-AA topologies for ATP
Hi, I recently made up a topology for ADP. You can probably modify it to ATP easily. I used native OPLS atom types based on the DNA parameters (http://rnp-group.genebee.msu.su/3d/ff.htm ). The charges are copied from CHARMM27. Also, there is one dihedral angle missing, again, copied from CHARMM. Please let me know if you have any question, suggestion, Cheers, Bin === In the ffoplsaa.rtp file, I added: [ ADP ] [ atoms ] PBopls_440 1.100 0 ;P O1Bopls_441 -0.900 1 ;O O2Bopls_441 -0.900 2 ;O O3Bopls_441 -0.900 3 ;O PAopls_440 1.500 4 ;P O1Aopls_441 -0.820 5 ;O2 O2Aopls_441 -0.820 6 ;O2 O3Aopls_442 -0.740 7 ;OS O5'opls_442 -0.620 8 ;OS C5'opls_443 -0.080 9 ;CT H5''opls_444 0.09010 ;HC H5' opls_444 0.09011 ;HC C4'opls_158 0.16012 ;CT H4'opls_156 0.09013 ;HC O4'opls_180 -0.50014 ;OS C1'opls_158 0.16015 ;CT H1'opls_156 0.09016 ;HC N9opls_354 -0.05017 ;NA C8opls_353 0.34018 ;CK H8opls_359 0.12019 ;H5 N7opls_352 -0.71020 ;NB C5opls_350 0.28021 ;CB C6opls_351 0.46022 ;CA N6opls_356 -0.77023 ;N2 H61opls_357 0.38024 ;H H62opls_358 0.38025 ;H N1opls_346 -0.74026 ;NC C2opls_347 0.50027 ;CQ H2opls_355 0.13028 ;H5 N3opls_348 -0.75029 ;NC C4opls_349 0.43030 ;CB C2'opls_158 0.14031 ;CT H2''opls_156 0.09032 ;HC O2'opls_171 -0.66033 ;OH H2'opls_172 0.43034 ;HO C3'opls_158 0.14035 ;CT H3'opls_156 0.09036 ;HC O3'opls_171 -0.66037 ;OS H3Topls_172 0.43038 [ bonds ] PBO3A PBO1B PBO2B PBO3B O3A PA PAO1A PAO2A PAO5' O3'H3T O5'C5' C5'C4' C4'O4' C4'C3' O4'C1' C1' N9 C1'C2' N9 C4 N9 C8 C4 N3 C2 N1 C6 N6 N6H61 N6H62 C6 C5 C5 N7 C2'C3' C2'O2' O2'H2' C3'O3' C1'H1' C2' H2'' C3'H3' C4'H4' C5'H5' C5' H5'' C8 H8 C2 H2 N1 C6 N3 C2 C4 C5 N7 C8 === === In the ffoplsaabon.itp file, I added: ; copied from ffoplsaanr [ angletypes ] NA CT OS 1 109.500418.680 ; DNA DCY [ dihedraltypes ] ; these are again copied from ffoplsaanr NA C CM CT 3 30.35430 0.0 -30.35430 0.0 0.0 0.0 ; aromatic ring DNA DTH C CM CT HC 3 -0.77874 -2.33623 0.0 3.11498 0.0 0.0 ; aromatic ring DNA DTH HC CT CT NA 3 0.97134 2.91401 0.0 -3.88535 0.0 0.0 ; RNA NA CT CT OH 3 16.74720 -16.74720 0.0 0.0 0.0 0.0 ; RNA CM NA CT OS 3 -3.14010 -3.14010 6.28020 0.0 0.0 0.0 ; DNA DCY C NA CT OS 3 -3.14010 -3.14010 6.28020 0.0 0.0 0.0 ; DNA DCY CT OS CT NA 3 -5.23350 7.32690 6.28020 -8.37360 0.0 0.0 ; [ dihedraltypes ] ; copied from charmm O2 POS P 1 0.0 0.12553.0 O2 POS P 1 0.0 0.41842.0 OS POS P 1 0.0 0.12553.0 OS POS P 1 0.0 0.12552.0 === On Jun 22, 2010, at 5:07 AM, Efrat Noy wrote: Hi, Does anyone have OPLS-AA topologies for ATP? Thanks, Efrat -- 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] 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 bruced...@yahoo.com wrote: On Wednesday, February 25, 2009 12:06:20 AM, Lucio Ricardo Montero Valenzuela lucio...@ibt.unam.mx 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.
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 t.pig...@bristol.ac.uk 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 bruced...@yahoo.com wrote: On Wednesday, February 25, 2009 12:06:20 AM, Lucio Ricardo Montero Valenzuela lucio...@ibt.unam.mx 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
Re: [gmx-users] OPLS-AA topologies for ATP/ADP.
Thanks very much. Lucio Montero. -- From: Justin A. Lemkul jalem...@vt.edu Sent: Wednesday, February 25, 2009 5:55 AM To: Discusson list for GROMACS users gmx-users@gromacs.org 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
[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
