Re: [gmx-users] PRODRG server issues
On 5/22/12 8:49 PM, rainy908 wrote: All: I know this question isn't particularly related to GROMACS, but I've contacted the PRODRG admin in the past have never received a response. That said, is anyone experiencing technical issues acquiring a token to use PRODRG after entering an email address? http://davapc1.bioch.dundee.ac.uk/prodrg/submit.html I've tried a variety of email addresses, academic and personal, only to receive the message: Forbidden You don't have permission to access /cgi-bin/xprodrg/gettoken on this server. I'm not sure whether the issue is particular to my IP address. Has anyone experienced this problem before? It sounds like a problem with server settings. Why not try ATB? The results will probably be better than what PRODRG gives you: http://compbio.biosci.uq.edu.au/atb/ -Justin -- Justin A. Lemkul, Ph.D. Research Scientist 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PRODRG charges
Hi Many thanks for your reply and sorry to come back on this. Is the fitting to experimental free energies of solvation, the only acceptable way to get GROMOS-compatible charges? Acceptable because this is the way that partial charges were derived for the gromos ff. In the quite usual case that these experimental data are not available for the ligand one is interested in, are DFT/ESP charges acceptable? Thanks again. George g...@bioacademy.gr wrote: Hello Given that the partial charges from PRODRG are not reliable (as explained Justin Lemkul's paper), are AM1-BCC charges calculated with the Chimera/Amber Tools a reasonable starting point? Yes, those charges are a reasonable start, but will almost certainly not be sufficient for the final topology. In this case, do we treat all ligand atoms as one charge group? Unless your ligand is 4 atoms or less, no. Please consult the manual regarding charge groups, and see existing Gromos96 building blocks for suitable charge groupings. -Justin -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PRODRG charges
On 2012-01-12 12:42, g...@bioacademy.gr wrote: Hi Many thanks for your reply and sorry to come back on this. Is the fitting to experimental free energies of solvation, the only acceptable way to get GROMOS-compatible charges? Acceptable because this is the way that partial charges were derived for the gromos ff. In the quite usual case that these experimental data are not available for the ligand one is interested in, are DFT/ESP charges acceptable? No. CHeck http://compbio.biosci.uq.edu.au/atb/ Thanks again. George g...@bioacademy.gr wrote: Hello Given that the partial charges from PRODRG are not reliable (as explained Justin Lemkul's paper), are AM1-BCC charges calculated with the Chimera/Amber Tools a reasonable starting point? Yes, those charges are a reasonable start, but will almost certainly not be sufficient for the final topology. In this case, do we treat all ligand atoms as one charge group? Unless your ligand is 4 atoms or less, no. Please consult the manual regarding charge groups, and see existing Gromos96 building blocks for suitable charge groupings. -Justin -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PRODRG charges
g...@bioacademy.gr wrote: Hello Given that the partial charges from PRODRG are not reliable (as explained Justin Lemkul's paper), are AM1-BCC charges calculated with the Chimera/Amber Tools a reasonable starting point? Yes, those charges are a reasonable start, but will almost certainly not be sufficient for the final topology. In this case, do we treat all ligand atoms as one charge group? Unless your ligand is 4 atoms or less, no. Please consult the manual regarding charge groups, and see existing Gromos96 building blocks for suitable charge groupings. -Justin -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PRODRG server
swati patel wrote: Hello Justin, Sorry for again and again bothering you.But in prodrg2.5 server,there is no option to choose force fields.It automatically generates topology in gromos 87 force fields. The default force field used by the latest PRODRG is Gromos96 43a1, not Gromos87. -Justin -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PRODRG topology
Marzinek, Jan wrote: Dear Gromacs Users, I used PRODRG server in order to obtain the topology file for my molecule (52 atoms with all hydrogens). However, server generated Gromacs topology which involves 47 atoms (for PDB file with polar/aromatic hydrogens). Whether I will use the pdb file with missing 4 hydrogen that wont be a good apporximation. How to overcome this? The Gromos96 force fields are united-atom force fields and may not use all the H atoms your input coordinates did. If you suspect some issue with protonation state, PRODRG can be forced into certain protonation with the ADDHYD or DELHYD keywords. Be advised, of course, of the usual caveats regarding the quality of PRODRG topologies: http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips -Justin -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PRODRG tools
Liu Shiyong wrote: Dear all, Is there any other free tool like PRODRG ? PRODRG server couldn't read PDB file from user any more. It 's not easy to get a free version asap. You can contact the maintainers for a standalone version of PRODRG. Then you can run it whenever you want. -Justin -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PRODRG tools
Actually, you can use other parametrization tools like antechamber (for amber) or cgenff (for charmm). Liu Shiyong wrote: Dear all, Is there any other free tool like PRODRG ? PRODRG server couldn't read PDB file from user any more. It 's not easy to get a free version asap. You can contact the maintainers for a standalone version of PRODRG. Then you can run it whenever you want. -Justin -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- Jorge R. Quintero Químico Universidad Industrial de Santander Bucaramanga, Santander - Colombia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PRODRG
Dear Dr.Justin I did it,it works.Thanks. there are another problem: I want to add some hydogens to my topology. I used ADDHYD atomname,But this dosen't work. PLease let me know how can I include some Hydrogenes in my topology. Thanks in advance Mohsen On Thu, Feb 10, 2011 at 7:56 PM, Justin A. Lemkul jalem...@vt.edu wrote: mohsen ramezanpour wrote: Dear Dr.Justin I have read this section before. There are 2 problem: 1:ADDHYD atomname and DELHYD atomname commands dosen't work! they result in ERROR in PRODRG You have to run PRODRG twice. The first time, you get the wrong output. Note the atom name that PRODRG assigns to your N atom. The second time, use DELHYD (name). If that doesn't work, then I have no idea and you're better off submitting your question to the PRODRG developers. 2:Actually I don't know the additional hydrogen is necessary or not! Because it may be necessary for proper protonation. My drug(Sertraline) is in a solvent,it may interact with water molecules and Nitrogen may get an additional hydrogen. A doubly-protonated secondary amine would be a fairly strong acid. You should do a pKa calculation to determine what is relevant rather than guessing. There are web servers and other software out there that can do this for you. Google is your friend. -Justin What do you think? On Wed, Feb 9, 2011 at 9:39 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: The OP's question is easily answered by referring to the PRODRG FAQ in dealing with proper protonation. As for Antechamber and the like, these are good tools, but do not produce GROMOS-compatible topologies, if that is indeed the underlying goal. We've done thorough analysis of various QM calculation methods for GROMOS charges, and none of them produce completely satisfactory topologies. Antechamber, Spartan, Gaussian, etc are good for initial charge calculations, but IMHO do not qualify as an end result for GROMOS parameterization due to the empirical refinement used in the force field derivation. All of that makes GROMOS parameterization somewhat tricky, and hence why force field choice is so incredibly important when designing projects... ;) -Justin TJ Mustard wrote: Yes I would recommend acpype. On February 9, 2011 at 9:42 AM jorge_quint...@ciencias.uis.edu.co mailto:jorge_quint...@ciencias.uis.edu.co wrote: I think that is better to use antechamber tools. On 10/02/2011 3:40 AM, mohsen ramezanpour wrote: Dear Users I am using PRODRG to make topology for my drug It addes Hydrogenes but in wrong way. My Nitrogen atom is bonded to 2 Carbos, and PRODRG addes 2 Hydrogenes to it . Please let me know how can I do. Thanks in advance This is not really the forum to get help about that. You need to read how to PRODRG needs input, and supply something it can deal with. Then do a whole bunch more work testing what it produced. Mark -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- Jorge R. Quintero Químico Universidad Industrial de Santander Bucaramanga, Santander - Colombia -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists TJ Mustard Email: musta...@onid.orst.edu mailto:musta...@onid.orst.edu -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
Re: [gmx-users] PRODRG
mohsen ramezanpour wrote: Dear Dr.Justin I did it,it works.Thanks. there are another problem: I want to add some hydogens to my topology. I used ADDHYD atomname,But this dosen't work. PLease let me know how can I include some Hydrogenes in my topology. Use a different force field and don't use PRODRG. Gromos96 is a united-atom force field. -Justin Thanks in advance Mohsen On Thu, Feb 10, 2011 at 7:56 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: mohsen ramezanpour wrote: Dear Dr.Justin I have read this section before. There are 2 problem: 1:ADDHYD atomname and DELHYD atomname commands dosen't work! they result in ERROR in PRODRG You have to run PRODRG twice. The first time, you get the wrong output. Note the atom name that PRODRG assigns to your N atom. The second time, use DELHYD (name). If that doesn't work, then I have no idea and you're better off submitting your question to the PRODRG developers. 2:Actually I don't know the additional hydrogen is necessary or not! Because it may be necessary for proper protonation. My drug(Sertraline) is in a solvent,it may interact with water molecules and Nitrogen may get an additional hydrogen. A doubly-protonated secondary amine would be a fairly strong acid. You should do a pKa calculation to determine what is relevant rather than guessing. There are web servers and other software out there that can do this for you. Google is your friend. -Justin What do you think? On Wed, Feb 9, 2011 at 9:39 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: The OP's question is easily answered by referring to the PRODRG FAQ in dealing with proper protonation. As for Antechamber and the like, these are good tools, but do not produce GROMOS-compatible topologies, if that is indeed the underlying goal. We've done thorough analysis of various QM calculation methods for GROMOS charges, and none of them produce completely satisfactory topologies. Antechamber, Spartan, Gaussian, etc are good for initial charge calculations, but IMHO do not qualify as an end result for GROMOS parameterization due to the empirical refinement used in the force field derivation. All of that makes GROMOS parameterization somewhat tricky, and hence why force field choice is so incredibly important when designing projects... ;) -Justin TJ Mustard wrote: Yes I would recommend acpype. On February 9, 2011 at 9:42 AM jorge_quint...@ciencias.uis.edu.co mailto:jorge_quint...@ciencias.uis.edu.co mailto:jorge_quint...@ciencias.uis.edu.co mailto:jorge_quint...@ciencias.uis.edu.co wrote: I think that is better to use antechamber tools. On 10/02/2011 3:40 AM, mohsen ramezanpour wrote: Dear Users I am using PRODRG to make topology for my drug It addes Hydrogenes but in wrong way. My Nitrogen atom is bonded to 2 Carbos, and PRODRG addes 2 Hydrogenes to it . Please let me know how can I do. Thanks in advance This is not really the forum to get help about that. You need to read how to PRODRG needs input, and supply something it can deal with. Then do a whole bunch more work testing what it produced. Mark -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-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/Support/Mailing_Lists/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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Jorge R. Quintero Químico Universidad Industrial de Santander Bucaramanga, Santander -
Re: [gmx-users] PRODRG
On 11/02/2011 8:18 PM, mohsen ramezanpour wrote: Dear Dr.Justin I did it,it works.Thanks. there are another problem: I want to add some hydogens to my topology. I used ADDHYD atomname,But this dosen't work. PLease let me know how can I include some Hydrogenes in my topology. As Justin suggested, this is not the right forum for PRODRG advice. This forum is for GROMACS discussions. I can only suggest you read the PRODRG documentation. Mark Thanks in advance Mohsen On Thu, Feb 10, 2011 at 7:56 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: mohsen ramezanpour wrote: Dear Dr.Justin I have read this section before. There are 2 problem: 1:ADDHYD atomname and DELHYD atomname commands dosen't work! they result in ERROR in PRODRG You have to run PRODRG twice. The first time, you get the wrong output. Note the atom name that PRODRG assigns to your N atom. The second time, use DELHYD (name). If that doesn't work, then I have no idea and you're better off submitting your question to the PRODRG developers. 2:Actually I don't know the additional hydrogen is necessary or not! Because it may be necessary for proper protonation. My drug(Sertraline) is in a solvent,it may interact with water molecules and Nitrogen may get an additional hydrogen. A doubly-protonated secondary amine would be a fairly strong acid. You should do a pKa calculation to determine what is relevant rather than guessing. There are web servers and other software out there that can do this for you. Google is your friend. -Justin What do you think? On Wed, Feb 9, 2011 at 9:39 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: The OP's question is easily answered by referring to the PRODRG FAQ in dealing with proper protonation. As for Antechamber and the like, these are good tools, but do not produce GROMOS-compatible topologies, if that is indeed the underlying goal. We've done thorough analysis of various QM calculation methods for GROMOS charges, and none of them produce completely satisfactory topologies. Antechamber, Spartan, Gaussian, etc are good for initial charge calculations, but IMHO do not qualify as an end result for GROMOS parameterization due to the empirical refinement used in the force field derivation. All of that makes GROMOS parameterization somewhat tricky, and hence why force field choice is so incredibly important when designing projects... ;) -Justin TJ Mustard wrote: Yes I would recommend acpype. On February 9, 2011 at 9:42 AM jorge_quint...@ciencias.uis.edu.co mailto:jorge_quint...@ciencias.uis.edu.co mailto:jorge_quint...@ciencias.uis.edu.co mailto:jorge_quint...@ciencias.uis.edu.co wrote: I think that is better to use antechamber tools. On 10/02/2011 3:40 AM, mohsen ramezanpour wrote: Dear Users I am using PRODRG to make topology for my drug It addes Hydrogenes but in wrong way. My Nitrogen atom is bonded to 2 Carbos, and PRODRG addes 2 Hydrogenes to it . Please let me know how can I do. Thanks in advance This is not really the forum to get help about that. You need to read how to PRODRG needs input, and supply something it can deal with. Then do a whole bunch more work testing what it produced. Mark -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-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/Support/Mailing_Lists/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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Jorge R. Quintero Químico Universidad Industrial de Santander Bucaramanga, Santander - Colombia -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-users@gromacs.org
Re: [gmx-users] PRODRG
Dear Dr.Justin I have read this section before. There are 2 problem: 1:ADDHYD atomname and DELHYD atomname commands dosen't work! they result in ERROR in PRODRG 2:Actually I don't know the additional hydrogen is necessary or not! Because it may be necessary for proper protonation. My drug(Sertraline) is in a solvent,it may interact with water molecules and Nitrogen may get an additional hydrogen. What do you think? On Wed, Feb 9, 2011 at 9:39 PM, Justin A. Lemkul jalem...@vt.edu wrote: The OP's question is easily answered by referring to the PRODRG FAQ in dealing with proper protonation. As for Antechamber and the like, these are good tools, but do not produce GROMOS-compatible topologies, if that is indeed the underlying goal. We've done thorough analysis of various QM calculation methods for GROMOS charges, and none of them produce completely satisfactory topologies. Antechamber, Spartan, Gaussian, etc are good for initial charge calculations, but IMHO do not qualify as an end result for GROMOS parameterization due to the empirical refinement used in the force field derivation. All of that makes GROMOS parameterization somewhat tricky, and hence why force field choice is so incredibly important when designing projects... ;) -Justin TJ Mustard wrote: Yes I would recommend acpype. On February 9, 2011 at 9:42 AM jorge_quint...@ciencias.uis.edu.co wrote: I think that is better to use antechamber tools. On 10/02/2011 3:40 AM, mohsen ramezanpour wrote: Dear Users I am using PRODRG to make topology for my drug It addes Hydrogenes but in wrong way. My Nitrogen atom is bonded to 2 Carbos, and PRODRG addes 2 Hydrogenes to it . Please let me know how can I do. Thanks in advance This is not really the forum to get help about that. You need to read how to PRODRG needs input, and supply something it can deal with. Then do a whole bunch more work testing what it produced. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Jorge R. Quintero Químico Universidad Industrial de Santander Bucaramanga, Santander - Colombia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists TJ Mustard Email: musta...@onid.orst.edu -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PRODRG
mohsen ramezanpour wrote: Dear Dr.Justin I have read this section before. There are 2 problem: 1:ADDHYD atomname and DELHYD atomname commands dosen't work! they result in ERROR in PRODRG You have to run PRODRG twice. The first time, you get the wrong output. Note the atom name that PRODRG assigns to your N atom. The second time, use DELHYD (name). If that doesn't work, then I have no idea and you're better off submitting your question to the PRODRG developers. 2:Actually I don't know the additional hydrogen is necessary or not! Because it may be necessary for proper protonation. My drug(Sertraline) is in a solvent,it may interact with water molecules and Nitrogen may get an additional hydrogen. A doubly-protonated secondary amine would be a fairly strong acid. You should do a pKa calculation to determine what is relevant rather than guessing. There are web servers and other software out there that can do this for you. Google is your friend. -Justin What do you think? On Wed, Feb 9, 2011 at 9:39 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: The OP's question is easily answered by referring to the PRODRG FAQ in dealing with proper protonation. As for Antechamber and the like, these are good tools, but do not produce GROMOS-compatible topologies, if that is indeed the underlying goal. We've done thorough analysis of various QM calculation methods for GROMOS charges, and none of them produce completely satisfactory topologies. Antechamber, Spartan, Gaussian, etc are good for initial charge calculations, but IMHO do not qualify as an end result for GROMOS parameterization due to the empirical refinement used in the force field derivation. All of that makes GROMOS parameterization somewhat tricky, and hence why force field choice is so incredibly important when designing projects... ;) -Justin TJ Mustard wrote: Yes I would recommend acpype. On February 9, 2011 at 9:42 AM jorge_quint...@ciencias.uis.edu.co mailto:jorge_quint...@ciencias.uis.edu.co wrote: I think that is better to use antechamber tools. On 10/02/2011 3:40 AM, mohsen ramezanpour wrote: Dear Users I am using PRODRG to make topology for my drug It addes Hydrogenes but in wrong way. My Nitrogen atom is bonded to 2 Carbos, and PRODRG addes 2 Hydrogenes to it . Please let me know how can I do. Thanks in advance This is not really the forum to get help about that. You need to read how to PRODRG needs input, and supply something it can deal with. Then do a whole bunch more work testing what it produced. Mark -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- Jorge R. Quintero Químico Universidad Industrial de Santander Bucaramanga, Santander - Colombia -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists TJ Mustard Email: musta...@onid.orst.edu mailto:musta...@onid.orst.edu -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www
Re: [gmx-users] PRODRG
On 10/02/2011 3:40 AM, mohsen ramezanpour wrote: Dear Users I am using PRODRG to make topology for my drug It addes Hydrogenes but in wrong way. My Nitrogen atom is bonded to 2 Carbos, and PRODRG addes 2 Hydrogenes to it . Please let me know how can I do. Thanks in advance This is not really the forum to get help about that. You need to read how to PRODRG needs input, and supply something it can deal with. Then do a whole bunch more work testing what it produced. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PRODRG
I think that is better to use antechamber tools. On 10/02/2011 3:40 AM, mohsen ramezanpour wrote: Dear Users I am using PRODRG to make topology for my drug It addes Hydrogenes but in wrong way. My Nitrogen atom is bonded to 2 Carbos, and PRODRG addes 2 Hydrogenes to it . Please let me know how can I do. Thanks in advance This is not really the forum to get help about that. You need to read how to PRODRG needs input, and supply something it can deal with. Then do a whole bunch more work testing what it produced. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Jorge R. Quintero Químico Universidad Industrial de Santander Bucaramanga, Santander - Colombia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PRODRG
Yes I would recommend acpype. On February 9, 2011 at 9:42 AM jorge_quint...@ciencias.uis.edu.co wrote: I think that is better to use antechamber tools. On 10/02/2011 3:40 AM, mohsen ramezanpour wrote: Dear Users I am using PRODRG to make topology for my drug It addes Hydrogenes but in wrong way. My Nitrogen atom is bonded to 2 Carbos, and PRODRG addes 2 Hydrogenes to it . Please let me know how can I do. Thanks in advance This is not really the forum to get help about that. You need to read how to PRODRG needs input, and supply something it can deal with. Then do a whole bunch more work testing what it produced. Mark -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Cant post? Read http://www.gromacs.org/Support/Mailing_Lists -- Jorge R. Quintero Qumico Universidad Industrial de Santander Bucaramanga, Santander - Colombia -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please dont post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Cant post? Read http://www.gromacs.org/Support/Mailing_Lists TJ Mustard Email: musta...@onid.orst.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PRODRG
The OP's question is easily answered by referring to the PRODRG FAQ in dealing with proper protonation. As for Antechamber and the like, these are good tools, but do not produce GROMOS-compatible topologies, if that is indeed the underlying goal. We've done thorough analysis of various QM calculation methods for GROMOS charges, and none of them produce completely satisfactory topologies. Antechamber, Spartan, Gaussian, etc are good for initial charge calculations, but IMHO do not qualify as an end result for GROMOS parameterization due to the empirical refinement used in the force field derivation. All of that makes GROMOS parameterization somewhat tricky, and hence why force field choice is so incredibly important when designing projects... ;) -Justin TJ Mustard wrote: Yes I would recommend acpype. On February 9, 2011 at 9:42 AM jorge_quint...@ciencias.uis.edu.co wrote: I think that is better to use antechamber tools. On 10/02/2011 3:40 AM, mohsen ramezanpour wrote: Dear Users I am using PRODRG to make topology for my drug It addes Hydrogenes but in wrong way. My Nitrogen atom is bonded to 2 Carbos, and PRODRG addes 2 Hydrogenes to it . Please let me know how can I do. Thanks in advance This is not really the forum to get help about that. You need to read how to PRODRG needs input, and supply something it can deal with. Then do a whole bunch more work testing what it produced. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Jorge R. Quintero Químico Universidad Industrial de Santander Bucaramanga, Santander - Colombia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists TJ Mustard Email: musta...@onid.orst.edu -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PRODRG
I'm completely in agreement with that advice. To use antechamber tool, I recommend use force field for all the system. The OP's question is easily answered by referring to the PRODRG FAQ in dealing with proper protonation. As for Antechamber and the like, these are good tools, but do not produce GROMOS-compatible topologies, if that is indeed the underlying goal. We've done thorough analysis of various QM calculation methods for GROMOS charges, and none of them produce completely satisfactory topologies. Antechamber, Spartan, Gaussian, etc are good for initial charge calculations, but IMHO do not qualify as an end result for GROMOS parameterization due to the empirical refinement used in the force field derivation. All of that makes GROMOS parameterization somewhat tricky, and hence why force field choice is so incredibly important when designing projects... ;) -Justin TJ Mustard wrote: Yes I would recommend acpype. On February 9, 2011 at 9:42 AM jorge_quint...@ciencias.uis.edu.co wrote: I think that is better to use antechamber tools. On 10/02/2011 3:40 AM, mohsen ramezanpour wrote: Dear Users I am using PRODRG to make topology for my drug It addes Hydrogenes but in wrong way. My Nitrogen atom is bonded to 2 Carbos, and PRODRG addes 2 Hydrogenes to it . Please let me know how can I do. Thanks in advance This is not really the forum to get help about that. You need to read how to PRODRG needs input, and supply something it can deal with. Then do a whole bunch more work testing what it produced. Mark -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists -- Jorge R. Quintero QuÃmico Universidad Industrial de Santander Bucaramanga, Santander - Colombia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists TJ Mustard Email: musta...@onid.orst.edu -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- Jorge R. Quintero Químico Universidad Industrial de Santander Bucaramanga, Santander - Colombia -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PRODRG server
Dear Dr.justin Actually by doing this we are using two different force fields in one simulation. I had done it before and the result was that I discussed before in gmx-users(LINCS Error,Exploding system,Bad contacts between atoms) Then,this approch seems to doesn't work about my system. Then I want to find charges and charge groups for gromos 43A1 and replace them for my drug(to edit PRODRG file manually) and work totally in gromos 43A1. Unfortunately I can't obtain these parameter. Please let me have if you have it. Can I use some Ab Initio software for determining partial charges of my drug? for example ABINIT or Gaussian! Thanks in advance On Sat, Jan 22, 2011 at 8:03 PM, Justin A. Lemkul jalem...@vt.edu wrote: mohsen ramezanpour wrote: Ok then,I can use PRODRG server to generate .top and .gro files for drug. since it's reported charges are not very accurate ,we can replace all charges completely with them in 53A6(if was present). But it means we are working in 53A6 force field. then,we must generate .top and .gro files for our protein with 53A6 too. and work completely with 53A6. Am i right? thanks in advance That sounds like a reasonable approach. Be sure to validate the drug topology. In my experience, this procedure is pretty good, but you always have to convince reviewers... -Justin On Sat, Jan 22, 2011 at 4:43 PM, Justin A. Lemkul jalem...@vt.edumailto: jalem...@vt.edu wrote: mohsen ramezanpour wrote: Dear Justin I read your articles about PRODRG server,they were very useful. But I have a question: are charges of functional groups and generally other atom groups the same in all force fields? Because you have modified charges of your molecules by Gromos96 53A6 while prodrg server is generating topology files in 43A1. I want to know can I replace charges from gromos 53A6 or other forcefields? thanks in advance Charges are not the same between force fields. We did our study with 43A1 since that is what PRODRG purports to produce. I would say that our recommendations carry to other Gromos force fields, as well, but don't take charges from 43A1 and apply them to 53A6. Be consistent within the force field. The atom types produced by PRODRG are largely shared between 43A1 and 53A6, so if you *completely* replace all charges with those from 53A6, you should have a topology that is compatible with 53A6. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PRODRG server
On 24/01/2011 10:06 PM, mohsen ramezanpour wrote: Dear Dr.justin Actually by doing this we are using two different force fields in one simulation. I had done it before and the result was that I discussed before in gmx-users(LINCS Error,Exploding system,Bad contacts between atoms) Then,this approch seems to doesn't work about my system. Sounds like you've re-learned the lessons here: http://www.gromacs.org/Documentation/How-tos/Parameterization Then I want to find charges and charge groups for gromos 43A1 and replace them for my drug(to edit PRODRG file manually) and work totally in gromos 43A1. Unfortunately I can't obtain these parameter. Please let me have if you have it. Can I use some Ab Initio software for determining partial charges of my drug? for example ABINIT or Gaussian! You should choose a force field based on the likelihood of being able to successfully make your observations. You want one that has a record of useful performance on similar systems, for which you can develop reasonably reliable parameters readily, test them suitably, and run simulations smoothly. Don't presuppose the form of the solution. Mark Thanks in advance On Sat, Jan 22, 2011 at 8:03 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: mohsen ramezanpour wrote: Ok then,I can use PRODRG server to generate .top and .gro files for drug. since it's reported charges are not very accurate ,we can replace all charges completely with them in 53A6(if was present). But it means we are working in 53A6 force field. then,we must generate .top and .gro files for our protein with 53A6 too. and work completely with 53A6. Am i right? thanks in advance That sounds like a reasonable approach. Be sure to validate the drug topology. In my experience, this procedure is pretty good, but you always have to convince reviewers... -Justin On Sat, Jan 22, 2011 at 4:43 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: mohsen ramezanpour wrote: Dear Justin I read your articles about PRODRG server,they were very useful. But I have a question: are charges of functional groups and generally other atom groups the same in all force fields? Because you have modified charges of your molecules by Gromos96 53A6 while prodrg server is generating topology files in 43A1. I want to know can I replace charges from gromos 53A6 or other forcefields? thanks in advance Charges are not the same between force fields. We did our study with 43A1 since that is what PRODRG purports to produce. I would say that our recommendations carry to other Gromos force fields, as well, but don't take charges from 43A1 and apply them to 53A6. Be consistent within the force field. The atom types produced by PRODRG are largely shared between 43A1 and 53A6, so if you *completely* replace all charges with those from 53A6, you should have a topology that is compatible with 53A6. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing list gmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-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/Support/Mailing_Lists/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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
Re: [gmx-users] PRODRG server
mohsen ramezanpour wrote: Dear Dr.justin Actually by doing this we are using two different force fields in one simulation. I had done it before and the result was that I discussed before in gmx-users(LINCS Error,Exploding system,Bad contacts between atoms) Then,this approch seems to doesn't work about my system. Then I want to find charges and charge groups for gromos 43A1 and replace them for my drug(to edit PRODRG file manually) and work totally in gromos 43A1. Please keep your story consistent. In the last message, you said you wanted to work completely within 53A6, so I advised you on how to do that, now you say that you're trying to work completely within 43A1. Unfortunately I can't obtain these parameter. You certainly do have these parameters. 43A1 is part of the Gromacs installation; in the .rtp file you'll find all of the functional groups that were derived in 43A1, as applied to amino acids and a few other groups. Please let me have if you have it. Can I use some Ab Initio software for determining partial charges of my drug? for example ABINIT or Gaussian! My paper that you said you read has discussion and recommendations on this point. But be very clear: none of the QM methods we tested were able to reproduce the charges that are assigned to known functional groups since the Gromos parameterization methodology calls for empirical refinement. Thus, manual modification and thorough validation are always necessary. -Justin Thanks in advance On Sat, Jan 22, 2011 at 8:03 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: mohsen ramezanpour wrote: Ok then,I can use PRODRG server to generate .top and .gro files for drug. since it's reported charges are not very accurate ,we can replace all charges completely with them in 53A6(if was present). But it means we are working in 53A6 force field. then,we must generate .top and .gro files for our protein with 53A6 too. and work completely with 53A6. Am i right? thanks in advance That sounds like a reasonable approach. Be sure to validate the drug topology. In my experience, this procedure is pretty good, but you always have to convince reviewers... -Justin On Sat, Jan 22, 2011 at 4:43 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: mohsen ramezanpour wrote: Dear Justin I read your articles about PRODRG server,they were very useful. But I have a question: are charges of functional groups and generally other atom groups the same in all force fields? Because you have modified charges of your molecules by Gromos96 53A6 while prodrg server is generating topology files in 43A1. I want to know can I replace charges from gromos 53A6 or other forcefields? thanks in advance Charges are not the same between force fields. We did our study with 43A1 since that is what PRODRG purports to produce. I would say that our recommendations carry to other Gromos force fields, as well, but don't take charges from 43A1 and apply them to 53A6. Be consistent within the force field. The atom types produced by PRODRG are largely shared between 43A1 and 53A6, so if you *completely* replace all charges with those from 53A6, you should have a topology that is compatible with 53A6. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org mailto:gmx-users@gromacs.org mailto:gmx-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/Support/Mailing_Lists/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 mailto:gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists --
Re: [gmx-users] PRODRG server
mohsen ramezanpour wrote: Thanks for your guidance. I looked that file,But I think the name of functional groups are different in .rtp file because I can't find no one of them in this file. Functional group names are not in the .rtp files. You locate applicable functional groups by knowing the residues in which they occur. please let me know how can I know the correct name f or functional groups for example:HYDROXYL,CARBOXYL,HALO,AMINO and ... All of these except halogens exist in common amino acids. If you have many non-standard groups (i.e. those that don't typically occur in biomolecules), then perhaps your choice of force field was a poor one. As Mark said, don't presuppose the solution. -Justin Thanks in advance for your help On Mon, Jan 24, 2011 at 4:01 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: mohsen ramezanpour wrote: Dear Dr.justin Actually by doing this we are using two different force fields in one simulation. I had done it before and the result was that I discussed before in gmx-users(LINCS Error,Exploding system,Bad contacts between atoms) Then,this approch seems to doesn't work about my system. Then I want to find charges and charge groups for gromos 43A1 and replace them for my drug(to edit PRODRG file manually) and work totally in gromos 43A1. Please keep your story consistent. In the last message, you said you wanted to work completely within 53A6, so I advised you on how to do that, now you say that you're trying to work completely within 43A1. Unfortunately I can't obtain these parameter. You certainly do have these parameters. 43A1 is part of the Gromacs installation; in the .rtp file you'll find all of the functional groups that were derived in 43A1, as applied to amino acids and a few other groups. Please let me have if you have it. Can I use some Ab Initio software for determining partial charges of my drug? for example ABINIT or Gaussian! My paper that you said you read has discussion and recommendations on this point. But be very clear: none of the QM methods we tested were able to reproduce the charges that are assigned to known functional groups since the Gromos parameterization methodology calls for empirical refinement. Thus, manual modification and thorough validation are always necessary. -Justin Thanks in advance On Sat, Jan 22, 2011 at 8:03 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: mohsen ramezanpour wrote: Ok then,I can use PRODRG server to generate .top and .gro files for drug. since it's reported charges are not very accurate ,we can replace all charges completely with them in 53A6(if was present). But it means we are working in 53A6 force field. then,we must generate .top and .gro files for our protein with 53A6 too. and work completely with 53A6. Am i right? thanks in advance That sounds like a reasonable approach. Be sure to validate the drug topology. In my experience, this procedure is pretty good, but you always have to convince reviewers... -Justin On Sat, Jan 22, 2011 at 4:43 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu mailto:jalem...@vt.edu wrote: mohsen ramezanpour wrote: Dear Justin I read your articles about PRODRG server,they were very useful. But I have a question: are charges of functional groups and generally other atom groups the same in all force fields? Because you have modified charges of your molecules by Gromos96 53A6 while prodrg server is generating topology files in 43A1. I want to know can I replace charges from gromos 53A6 or other forcefields? thanks in advance Charges are not the same between force fields. We did our study with 43A1 since that is what PRODRG purports to produce. I would say that our recommendations carry to other Gromos force fields, as well, but don't take charges from 43A1
Re: [gmx-users] PRODRG server
mohsen ramezanpour wrote: Dear Justin I read your articles about PRODRG server,they were very useful. But I have a question: are charges of functional groups and generally other atom groups the same in all force fields? Because you have modified charges of your molecules by Gromos96 53A6 while prodrg server is generating topology files in 43A1. I want to know can I replace charges from gromos 53A6 or other forcefields? thanks in advance Charges are not the same between force fields. We did our study with 43A1 since that is what PRODRG purports to produce. I would say that our recommendations carry to other Gromos force fields, as well, but don't take charges from 43A1 and apply them to 53A6. Be consistent within the force field. The atom types produced by PRODRG are largely shared between 43A1 and 53A6, so if you *completely* replace all charges with those from 53A6, you should have a topology that is compatible with 53A6. -Justin -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PRODRG server
Ok then,I can use PRODRG server to generate .top and .gro files for drug. since it's reported charges are not very accurate ,we can replace all charges completely with them in 53A6(if was present). But it means we are working in 53A6 force field. then,we must generate .top and .gro files for our protein with 53A6 too. and work completely with 53A6. Am i right? thanks in advance On Sat, Jan 22, 2011 at 4:43 PM, Justin A. Lemkul jalem...@vt.edu wrote: mohsen ramezanpour wrote: Dear Justin I read your articles about PRODRG server,they were very useful. But I have a question: are charges of functional groups and generally other atom groups the same in all force fields? Because you have modified charges of your molecules by Gromos96 53A6 while prodrg server is generating topology files in 43A1. I want to know can I replace charges from gromos 53A6 or other forcefields? thanks in advance Charges are not the same between force fields. We did our study with 43A1 since that is what PRODRG purports to produce. I would say that our recommendations carry to other Gromos force fields, as well, but don't take charges from 43A1 and apply them to 53A6. Be consistent within the force field. The atom types produced by PRODRG are largely shared between 43A1 and 53A6, so if you *completely* replace all charges with those from 53A6, you should have a topology that is compatible with 53A6. -Justin -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PRODRG server
mohsen ramezanpour wrote: Ok then,I can use PRODRG server to generate .top and .gro files for drug. since it's reported charges are not very accurate ,we can replace all charges completely with them in 53A6(if was present). But it means we are working in 53A6 force field. then,we must generate .top and .gro files for our protein with 53A6 too. and work completely with 53A6. Am i right? thanks in advance That sounds like a reasonable approach. Be sure to validate the drug topology. In my experience, this procedure is pretty good, but you always have to convince reviewers... -Justin On Sat, Jan 22, 2011 at 4:43 PM, Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu wrote: mohsen ramezanpour wrote: Dear Justin I read your articles about PRODRG server,they were very useful. But I have a question: are charges of functional groups and generally other atom groups the same in all force fields? Because you have modified charges of your molecules by Gromos96 53A6 while prodrg server is generating topology files in 43A1. I want to know can I replace charges from gromos 53A6 or other forcefields? thanks in advance Charges are not the same between force fields. We did our study with 43A1 since that is what PRODRG purports to produce. I would say that our recommendations carry to other Gromos force fields, as well, but don't take charges from 43A1 and apply them to 53A6. Be consistent within the force field. The atom types produced by PRODRG are largely shared between 43A1 and 53A6, so if you *completely* replace all charges with those from 53A6, you should have a topology that is compatible with 53A6. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu http://vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PRODRG server
mohsen ramezanpour wrote: Dear All I generated toplogy file for a drug by PRODG server. How can I validate it? i looked at these links but there are not a way for doing that. http://www.gromacs.org/Documentation/How-tos/Parameterization http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips thanks in advance The Gromacs site is not going to be a comprehensive, how-to-do-everything site. If you're using a certain force field, you should have based that choice on an understanding of how that force field was derived, its inherent assumptions, limitations, etc. Refer to the original literature for whichever parameter set you want to use for parameterization methodology. That said, Gromos parameterization is a bit vague, although the basics are certainly described in the literature. Did you read the paper linked from http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips? There are tips there. Another of my papers (shameless self-promotion, sorry) has an example of how I treated one particular molecule, as an example: http://pubs.acs.org/doi/abs/10.1021/bi1000855 -Justin -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
Re: [gmx-users] PRODRG crash
Moeed wrote: Dear Justin, Actually, I used -d option because you said the atoms in the box must be half a bond length from the edges of box...I thought maybe this can be done by -d... My point was that you should not be using a combination of -box, -d, and -angles simultaneously. Use either -box or -d, not both, and don't use -angles. With PRODRG I am unable to produce coordinate file a chain with less than three C atoms. I sketched the molecules: C-C ethane C=C Ethylene but I am getting a message: ERRDRG PRODRG does not deal with mono/di-atomic molecules. PRODRG Program terminated unsuccessfully, sorry! 1- Could you please help me with this. (actually I need structure file of ethylene in the future) So make a 4-carbon repeat unit. It's easy to draw chains with PRODRG (but there is a limitation to the number of atoms). -Justin 2- How can I generate structure file of repeating unit -CH2-CH2- with PRODRG. I tried the followings...and all I am getting is the above message.. :( H H | | C-C | | H H H H | | -C-C- | | H H -C-C- Moeed -- 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] PRODRG
Smith, Chanel Chonda wrote: In the drug-enzyme tutorial it says that the crude was refined using a certain force field, SD, and CG. How was this accomplished? Then parameters from that force field (like charges and charge groups from analogous functional groups) were probably assigned, followed by energy minimization. -Justin -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Wed 10/7/2009 1:11 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] PRODRG jorge_quint...@ciencias.uis.edu.co wrote: Hello Chanel Could you send a copy of the PDB file. I think that the error is related with label atoms included in each force fiel parameter. More likely this is yet another case of a common misconception about how to use Gromacs. Specifically, the first error message located under the pdb2gmx heading here: http://www.gromacs.org/Documentation/Errors -Justin See you. Hello, I have recently made a pdb file using the Dundee PRODRG server. However, when I try to use this pdb in gromacs, I receive an error message that states: DRG is not in the topology database. I have tried to use the available tutorial to solve this issue, but with not much success. Could anyone give me a step by step procedure so that I can use the pdb I have made using PRODRG? Thanks, Chanel King ___ 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 -- 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] PRODRG
Smith, Chanel Chonda wrote: Hello, I have recently made a pdb file using the Dundee PRODRG server. However, when I try to use this pdb in gromacs, I receive an error message that states: DRG is not in the topology database. I have tried to use the available tutorial to solve this issue, but with not much success. Could anyone give me a step by step procedure so that I can use the pdb I have made using PRODRG? The purpose of PRODRG is to generate the topology, such that you don't have to pass it through pdb2gmx. If the molecule doesn't exist in the force field .rtp file, then you will get this error. John Kerrigan's tutorial explains how to use the PRODRG topology within your system .top quite clearly. Be advised that the charges and charge groups produced by PRODRG are often unsatisfactory, requiring manual modification and validation. -Justin Thanks, Chanel King ___ 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] PRODRG
Hello Chanel Could you send a copy of the PDB file. I think that the error is related with label atoms included in each force fiel parameter. See you. Hello, I have recently made a pdb file using the Dundee PRODRG server. However, when I try to use this pdb in gromacs, I receive an error message that states: DRG is not in the topology database. I have tried to use the available tutorial to solve this issue, but with not much success. Could anyone give me a step by step procedure so that I can use the pdb I have made using PRODRG? Thanks, Chanel King ___ 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] PRODRG
jorge_quint...@ciencias.uis.edu.co wrote: Hello Chanel Could you send a copy of the PDB file. I think that the error is related with label atoms included in each force fiel parameter. More likely this is yet another case of a common misconception about how to use Gromacs. Specifically, the first error message located under the pdb2gmx heading here: http://www.gromacs.org/Documentation/Errors -Justin See you. Hello, I have recently made a pdb file using the Dundee PRODRG server. However, when I try to use this pdb in gromacs, I receive an error message that states: DRG is not in the topology database. I have tried to use the available tutorial to solve this issue, but with not much success. Could anyone give me a step by step procedure so that I can use the pdb I have made using PRODRG? Thanks, Chanel King ___ 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 -- 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] PRODRG
In the drug-enzyme tutorial it says that the crude was refined using a certain force field, SD, and CG. How was this accomplished? -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Wed 10/7/2009 1:11 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] PRODRG jorge_quint...@ciencias.uis.edu.co wrote: Hello Chanel Could you send a copy of the PDB file. I think that the error is related with label atoms included in each force fiel parameter. More likely this is yet another case of a common misconception about how to use Gromacs. Specifically, the first error message located under the pdb2gmx heading here: http://www.gromacs.org/Documentation/Errors -Justin See you. Hello, I have recently made a pdb file using the Dundee PRODRG server. However, when I try to use this pdb in gromacs, I receive an error message that states: DRG is not in the topology database. I have tried to use the available tutorial to solve this issue, but with not much success. Could anyone give me a step by step procedure so that I can use the pdb I have made using PRODRG? Thanks, Chanel King ___ 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 -- 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 winmail.dat___ 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] prodrg 4.5beta generated topologies and exclusions
Dean Cue bas wrote: Hello all. Just a quick clarification, please. Reading the original GROMOS53A6 paper, it appears that 2nd neighbor (1-3) interactions are always excluded, and that third neighbor (1-4) non-bonding interactions are used, yet modified in some circumstances. The paper also states that all (1-4) interactions should be explicitly excluded for atoms either within or directly bonded to aromatic rings to help keep planarity. I could confirm this in the adenine topology in the ffG53a6.rtp file where there were the above described exclusions in the [exclusions] section for that residue. Now my questions. Prodrg4.5beta produces .itp files for all my ligands where under the [moleculetype] section it states that nrexcl is 3. Doesn’t this automatically exclude all (1-4) interactions for that ligand? Yes, such interactions are excluded. If so, then doesn’t that automatically negate the need to explicitly exclude the (1-4) interactions for planar aromatic systems as described above in the ff paper? The authors of that paper were probably not pre-supposing the use of any particular topology-generation tool. If so, then doesn’t excluding all these third neighbor (1-4) interactions for ligand topologies produced by Prodrg ignore intra-molecular interactions that are important in the simulated behavior and properties of these ligands? It would seem so. If this bothered me, I would start by reading the PRODRG documentation - but I would have done that before using anything it generated. Doesn’t this imply that the default for ffG53a6 intra-molecular protein-atom/protein-atom non-bonded interactions is nrexcl =2 ? That might depend on the mechanism that is being used for the different and/or missing 1-4 interactions. Pre-excluding and then adding might be easier than pre-including and then excluding. Thanks in advance for any clarification in this area. I just want to be sure I’m accounting for my exclusions properly. Mark ___ 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] prodrg
Bhawana Gupta wrote: hello everyone, Pls tell me whether we can use PRODRG server only for generating peptides with unusual amino acid through JME or it can be used for the peptides having usual amino acid. PRODRG is most useful in obtaining topologies for small molecules. You might use it to get the initial topology for an unusual amino acid, but you would probably be best to translate that topology into an .rtp file for yourself. Be aware that the charges and charge groups generated by PRODRG typically require refinement and thorough validation of the parameters. whether it is necessary to use pdb2gmx for peptide containing usual amino acid or we can do it with PRODRG server also. Well, you could write your topology by hand, if you really wanted to :) But pdb2gmx makes life quite simple for generating topologies of proteins and peptides. -Justin Pls help me out. Bhawana ___ 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 [EMAIL PROTECTED] 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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] prodrg and charge groups
Diane, I can't speak to charge groups, but in terms of charges, I think I remember that prodrg has a number of disclaimers about its charges. Personally, I would be rather reluctant to use prodrg charges for simulating ligands. A fast alternative would be to download the Antechamber package, which can calculate am1-bcc charges, and run pdb's/mol2 files for your molecules through it to get charges output to a mol2 file, then write a little script to take these charges and use them in your topology instead of those from prodrg. Although am1-bcc charges are semi-empirical, we've been doing a pretty extensive test of charge sets (including QM potentials from various levels of theory fit with RESP) across a large series (well, 40-ish) of molecules and are finding that am1-bcc charges actually give hydration free energies that are in the best agreement with experiment (RMS error about 1 kcal/mol in TIP3P). The best QM calcs roughly comparable in terms of RMS error, but are obviously substantially more demanding. Best wishes, David Mobley UCSF On 6/29/06, Diane Fournier [EMAIL PROTECTED] wrote: I don't know if this has already been discussed, but I'm wondering how the charges and charge groups are assigned by PRODRG. I'm curious about this because I have been using it for a few similar ligands which all contain a steroid (estradiol) moiety. In the three cases, the charge groups and charges that were assigned were quite different for the estradiol part. Also, when compared to the partial charges found for the phenol group of tyrosine in the amino acid topologies, the phenol group charges for estradiol make no sense (they should be quite similar, right ?). What I've been doing until now is to modify the charges and charge groups so that they are identical for the estradiol moiety in all cases (so that this part displays the same behavior in all simulations). Is this the right way to proceed ? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] 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 don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
