Re: [gmx-users] Topology file for phosphothreonine (TPO) for OPLS force field
Antoine Delmotte wrote: Thank you very much for your quick response, Justin. I guess I need a little bit more practise to make the parametrization myself. Do you have any clues on where I could find published parameters? Are there databases for this or something similar? Literature searching is your best bet. But as far as I know, there is no database of previously-published parameters. Understanding the intrinsics of the force field (the original derivation and subsequent improvements) will be the most useful for you to understand the intrinsics of the force field. If you're dead set on using OPLS, then you probably have (a lot) of work cut out for you. Parameters for phosphorylated Ser, Thr, and Tyr for Gromos96 43a1 were published some time ago. -Justin Regards, Antoine Le 5/02/2010 18:23, Justin A. Lemkul a écrit : Antoine Delmotte wrote: Dear gmx-users, I would like to simulate the CDK9 protein (3BLH in PDB), but there is one residue (TPO, phosphothreonine), which Gromacs does not recognise. I found the PRODRG website as well as force field parameters for TPO for the Gromos96.1 force field. However, I would like to use the OPLS-AA force field. I therefore need a topology file for this force field, which cannot be provided by PRODRG (only useful for united atoms force fields). Does anyone have an idea about where I could get the phosphothreonine itp file for OPLS force field? Search the literature to see if anyone has published parameters for it. Otherwise, could someone give me clues or the link to a good tutorial about how to create this itp file myself? That's what Chapter 5 of the manual is for, provided you have reliable parameters (see below). Molecular dynamics is something completely new for me so, sorry if I ask stupid questions. It also seems I am not the first one to have this problem but I could not find any solution on the archive of the mailing list. If MD is completely new to you, and you are unable to find previously published and validated parameters, the parameterization of a new species is likely not a suitable task. Parameterization is an expert topic, and it can take many months or years to develop reliable parameters, even if you know what you are doing at the very start. Be forewarned: http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin I thank you in advance. Best regards, Antoine Hotmail : une messagerie fiable avec la protection anti-spam performante de Microsoft Inscrivez-vous https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] Topology file for phosphothreonine (TPO) for OPLS force field
Thank you very much for your quick response, Justin. I guess I need a little bit more practise to make the parametrization myself. Do you have any clues on where I could find published parameters? Are there databases for this or something similar? Regards, Antoine Le 5/02/2010 18:23, Justin A. Lemkul a écrit : Antoine Delmotte wrote: Dear gmx-users, I would like to simulate the CDK9 protein (3BLH in PDB), but there is one residue (TPO, phosphothreonine), which Gromacs does not recognise. I found the PRODRG website as well as force field parameters for TPO for the Gromos96.1 force field. However, I would like to use the OPLS-AA force field. I therefore need a topology file for this force field, which cannot be provided by PRODRG (only useful for united atoms force fields). Does anyone have an idea about where I could get the phosphothreonine itp file for OPLS force field? Search the literature to see if anyone has published parameters for it. Otherwise, could someone give me clues or the link to a good tutorial about how to create this itp file myself? That's what Chapter 5 of the manual is for, provided you have reliable parameters (see below). Molecular dynamics is something completely new for me so, sorry if I ask stupid questions. It also seems I am not the first one to have this problem but I could not find any solution on the archive of the mailing list. If MD is completely new to you, and you are unable to find previously published and validated parameters, the parameterization of a new species is likely not a suitable task. Parameterization is an expert topic, and it can take many months or years to develop reliable parameters, even if you know what you are doing at the very start. Be forewarned: http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin I thank you in advance. Best regards, Antoine Hotmail : une messagerie fiable avec la protection anti-spam performante de Microsoft Inscrivez-vous https://signup.live.com/signup.aspx?id=60969 -- 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] Topology file for phosphothreonine (TPO) for OPLS force field
Thank you very much for this, Bruce. It will help me, for sure. Could you just let me know where you found the parameters or how you generated them? Thanks in advance. Regards, Antoine Le 5/02/2010 22:39, Bruce D. Ray a écrit : On Fri, February 5, 2010 at 1:06:34 PM, Antoine Delmotte antoinedelmo...@hotmail.com wrote: I would like to simulate the CDK9 protein (3BLH in PDB), but there is one residue (TPO, phosphothreonine), which Gromacs does not recognise. I found the PRODRG website as well as force field parameters for TPO for the Gromos96.1 force field. However, I would like to use the OPLS-AA force field. I therefore need a topology file for this force field, which cannot be provided by PRODRG (only useful for united atoms force fields). Does anyone have an idea about where I could get the phosphothreonine itp file for OPLS force field? Otherwise, could someone give me clues or the link to a good tutorial about how to create this itp file myself? Molecular dynamics is something completely new for me so, sorry if I ask stupid questions. It also seems I am not the first one to have this problem but I could not find any solution on the archive of the mailing list. The charges probably need a little more work, but this might be a start towards an rtp file for phosphothreonine to add to ffoplsaa.rtp. [ TPO ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B 0.140 1 HAopls_1400.060 1 CBopls_1580.205 2 HBopls_1400.060 2 OG1opls_447 -0.700 2 Popls_4451.795 3 O1Popls_446 -1.120 3 O2Popls_446 -1.120 3 O3Popls_446 -1.120 3 CG2opls_135 -0.180 4 HG21opls_1400.060 4 HG22opls_1400.060 4 HG23opls_1400.060 4 Copls_2350.500 5 Oopls_236 -0.500 5 [ bonds ] N H NCA CAHA CACB CA C CBHB CB OG1 CB CG2 OG1 P O1P P O2P P O3P P CG2 HG21 CG2 HG22 CG2 HG23 C O -C N [ dihedrals ] ; override some of the typebased dihedrals NCACB OG1dih_SER_THR_chi1_N_C_C_O CCACB OG1dih_SER_THR_chi1_CO_C_C_O CACB OG1 HG1dih_SER_THR_chi2_C_C_OH_HO [ impropers ] -CCA N Himproper_Z_N_X_Y CA+N C Oimproper_O_C_X_Y I hope that helps. -- 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] Topology file for phosphothreonine (TPO) for OPLS force field
Thank you very much Fairuz. I will try this. Le 6/02/2010 1:20, fairuz zulkifli a écrit : to create itp file with OPLS force feild, you can try use GAMESS. -fairuz- -- 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] Topology file for phosphothreonine (TPO) for OPLS force field
On Sat, February 6, 2010 at 11:08:30 AM, Antoine Delmotte antoinedelmo...@hotmail.com wrote: Thank you very much for this, Bruce. It will help me, for sure. Could you just let me know where you found the parameters or how you generated them? Most of the parameters came from the entry for threonine in ffoplsaa.rtp The remainder came from running the most recent beta test version of topolbuild 1.3 with the command line /usr/local/bin/topolbuild -dir /usr/local/topolbuild -ff oplsaa -n tpo_pep -charge which generates an OPLSaa topology with parameters found originally in the Gromacs OPLSaa installation against a short peptide containing phosphothreonine and sets the atom charges to the OPLSaa atom type charges. I then edited the threonine entry from ffoplsaa.rtp according to add in the phosphate atom types, and change those atom types that are altered by the presence of the phosphate. Finally, I adjusted the charge on the phosphorous from the charge given in ffoplsaanb.itp in order to have the total charge come out as -2 for a fully ionized phosphate. The exact ionization would depend on pH, of course, and I would have to run the command for protonated TPO (TPH ? or TPH2 ? for the mono- and di-protonated species?) to further correct atom types and charges. -- 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] Topology file for phosphothreonine (TPO) for OPLS force field
Antoine Delmotte wrote: Dear gmx-users, I would like to simulate the CDK9 protein (3BLH in PDB), but there is one residue (TPO, phosphothreonine), which Gromacs does not recognise. I found the PRODRG website as well as force field parameters for TPO for the Gromos96.1 force field. However, I would like to use the OPLS-AA force field. I therefore need a topology file for this force field, which cannot be provided by PRODRG (only useful for united atoms force fields). Does anyone have an idea about where I could get the phosphothreonine itp file for OPLS force field? Search the literature to see if anyone has published parameters for it. Otherwise, could someone give me clues or the link to a good tutorial about how to create this itp file myself? That's what Chapter 5 of the manual is for, provided you have reliable parameters (see below). Molecular dynamics is something completely new for me so, sorry if I ask stupid questions. It also seems I am not the first one to have this problem but I could not find any solution on the archive of the mailing list. If MD is completely new to you, and you are unable to find previously published and validated parameters, the parameterization of a new species is likely not a suitable task. Parameterization is an expert topic, and it can take many months or years to develop reliable parameters, even if you know what you are doing at the very start. Be forewarned: http://www.gromacs.org/Documentation/How-tos/Parameterization -Justin I thank you in advance. Best regards, Antoine Hotmail : une messagerie fiable avec la protection anti-spam performante de Microsoft Inscrivez-vous https://signup.live.com/signup.aspx?id=60969 -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee 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] Topology file for phosphothreonine (TPO) for OPLS force field
On Fri, February 5, 2010 at 1:06:34 PM, Antoine Delmotte antoinedelmo...@hotmail.com wrote: I would like to simulate the CDK9 protein (3BLH in PDB), but there is one residue (TPO, phosphothreonine), which Gromacs does not recognise. I found the PRODRG website as well as force field parameters for TPO for the Gromos96.1 force field. However, I would like to use the OPLS-AA force field. I therefore need a topology file for this force field, which cannot be provided by PRODRG (only useful for united atoms force fields). Does anyone have an idea about where I could get the phosphothreonine itp file for OPLS force field? Otherwise, could someone give me clues or the link to a good tutorial about how to create this itp file myself? Molecular dynamics is something completely new for me so, sorry if I ask stupid questions. It also seems I am not the first one to have this problem but I could not find any solution on the archive of the mailing list. The charges probably need a little more work, but this might be a start towards an rtp file for phosphothreonine to add to ffoplsaa.rtp. [ TPO ] [ atoms ] Nopls_238 -0.500 1 Hopls_2410.300 1 CAopls_224B 0.140 1 HAopls_1400.060 1 CBopls_1580.205 2 HBopls_1400.060 2 OG1opls_447 -0.700 2 Popls_4451.795 3 O1Popls_446 -1.120 3 O2Popls_446 -1.120 3 O3Popls_446 -1.120 3 CG2opls_135 -0.180 4 HG21opls_1400.060 4 HG22opls_1400.060 4 HG23opls_1400.060 4 Copls_2350.500 5 Oopls_236 -0.500 5 [ bonds ] N H NCA CAHA CACB CA C CBHB CB OG1 CB CG2 OG1 P O1P P O2P P O3P P CG2 HG21 CG2 HG22 CG2 HG23 C O -C N [ dihedrals ] ; override some of the typebased dihedrals NCACB OG1dih_SER_THR_chi1_N_C_C_O CCACB OG1dih_SER_THR_chi1_CO_C_C_O CACB OG1 HG1dih_SER_THR_chi2_C_C_OH_HO [ impropers ] -CCA N Himproper_Z_N_X_Y CA+N C Oimproper_O_C_X_Y I hope that helps. -- 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] Topology file for phosphothreonine (TPO) for OPLS force field
to create itp file with OPLS force feild, you can try use GAMESS. -fairuz- -- 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
