[gmx-users] simulation of a protein including calcium ion
Dear Justin thanks for your attention in my case calcium ion is bonded to 4 oxygen atoms of C=O group of protein. yes, Calcium ions are present in nearly all the force fields in Gromacs. but there are only parameters in * nb.itp and not in * bon.itp. how to obtain these new parameters for my case? -- 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] simulation of a protein including calcium ion
leila karami wrote: Dear Justin thanks for your attention in my case calcium ion is bonded to 4 oxygen atoms of C=O group of protein. yes, Calcium ions are present in nearly all the force fields in Gromacs. but there are only parameters in * nb.itp and not in * bon.itp. how to obtain these new parameters for my case? Deriving new bonded parameters is not a simple task, and may or may not be appropriate. A coordination complex may be held in place by electrostatic interactions, or you may choose to use distance restraints to keep the bonded geometry in place. If you think that actual (chemical) bonds should be present, then there is not a suitable force field for you to use, since the charge transfer effects will invalidate the charges assigned to C=O groups by the force field. -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] simulation of a protein including calcium ion
Dear Justin Is there any way for this problem? -- 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] simulation of a protein including calcium ion
leila karami wrote: Dear Justin Is there any way for this problem? Please keep Tsjerk's comments (http://lists.gromacs.org/pipermail/gmx-users/2010-October/054938.html) in mind. If the calcium coordination complex plays only a minor structural role, you can probably justify using distance restraints (added to the topology after pdb2gmx). If it has some other functionally-significant role, then you have harder decisions to make. In either case, you should turn to the literature to understand how others typically address metal coordination complexes and make an educated choice that suits your needs best. Posting to the mailing list and getting a few tips should not take place of doing your homework thoroughly. -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] simulation of a protein including calcium ion
Hi gromacs users I want to study simulation of a protein including calcium ion. Can I use gromacs force fields? any help will highly appreciated. -- 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] simulation of a protein including calcium ion
Hi I think it is a typical ligand in your pdb file.what do you think? if it be a ligand you can use PRODRG server to make topology file for your ligand and you must edit other files. please read this article: GROMACS Tutorial for Drug – Enzyme Complex best mohsen On Sat, Oct 16, 2010 at 11:32 AM, mohsen ramezanpour ramezanpour.moh...@gmail.com wrote: Hi I think it is a typical ligand in your pdb file.what do you think? if it be a ligand you can use PRODRG server to make topology file for your ligand and you must edit other files. please read the attached article. best mohsen On Sat, Oct 16, 2010 at 11:04 AM, leila karami karami.lei...@gmail.comwrote: Hi gromacs users I want to study simulation of a protein including calcium ion. Can I use gromacs force fields? any help will highly appreciated. -- 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
[gmx-users] simulation of a protein including calcium ion
Dear mohsen ramezanpour* * yes. calcium is a typical ligand in my pdb file.I used PRODRG server to make topology file but ERRDRG Too many atoms in this molecule (should be =300). PRODRG Program terminated unsuccessfully, sorry! -- 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] simulation of a protein including calcium ion
Dear Leila Ok,But you have to separate your ions from your general pdb file(protein+ions) in the form of pdb, in the other words you need to obtain the pdb files for your ions separately and then paste it to PRODRG server.because your protein has more than 300 atoms alonly. I hope it can help you On Sat, Oct 16, 2010 at 12:00 PM, leila karami karami.lei...@gmail.comwrote: Dear mohsen ramezanpour* * yes. calcium is a typical ligand in my pdb file.I used PRODRG server to make topology file but ERRDRG Too many atoms in this molecule (should be =300). PRODRG Program terminated unsuccessfully, sorry! -- 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
[gmx-users] simulation of a protein including calcium ion
Dear mohsen ramezanpour my pdb file has 3000atoms (protein) + 1 atom (calcium). Should I separate ion from general pdb again? -- 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] simulation of a protein including calcium ion
Dear Leila Yes,I think so please read the article who I pointed,It can help you On Sat, Oct 16, 2010 at 12:16 PM, leila karami karami.lei...@gmail.comwrote: Dear mohsen ramezanpour my pdb file has 3000atoms (protein) + 1 atom (calcium). Should I separate ion from general pdb again? -- 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] simulation of a protein including calcium ion
leila karami wrote: Dear mohsen ramezanpour/ / yes. calcium is a typical ligand in my pdb file.I used PRODRG server to make topology file but ERRDRG Too many atoms in this molecule (should be =300). PRODRG Program terminated unsuccessfully, sorry! There is no need to invoke PRODRG for any of this. Calcium ions are present in nearly all the force fields in Gromacs, and require no special intervention - pdb2gmx can handle them. PRODRG is only useful for small molecule topologies, (which are usually not so accurate) so passing it an entire protein is not going to work (as you can see). It will also fail with an error if you pass it a single Ca ion. -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] simulation of a protein including calcium ion
Hi, Do mind that calcium binding may involve (quantum) effects that are ill captured by classical force fields. If the binding site plays a central role in your research question, this may be problematic. Cheers, Tsjerk On Oct 16, 2010 2:34 PM, Justin A. Lemkul jalem...@vt.edu wrote: leila karami wrote: Dear mohsen ramezanpour/ / yes. calcium is a typical ligand in my pdb ... There is no need to invoke PRODRG for any of this. Calcium ions are present in nearly all the force fields in Gromacs, and require no special intervention - pdb2gmx can handle them. PRODRG is only useful for small molecule topologies, (which are usually not so accurate) so passing it an entire protein is not going to work (as you can see). It will also fail with an error if you pass it a single Ca ion. -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 ... -- 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
