[gmx-users] RE: simulation of a metal binding sites
Hi, There are methodological difficulties in simulating multivalent ions together with proteins. Check the mailing list for a discussion and reference. This is not an issue of Gromacs but of dealing with protein-ion interactions using a classical non-polarisable force field. Check the literature. Ran. Message: 3 Date: Wed, 16 Feb 2011 20:14:07 -0800 From: bharat gupta bharat.85.m...@gmail.com Subject: [gmx-users] RE: simulation of a metal binding sites To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: aanlktin06ut6+wrfpz4a79fq9g-galmk35uxecph+...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi, I have incorporated some metal binding sites(zinc ion) in my protein. Now I want to see whether that region binds to zinc ions or not and what is the effect of ion binding to the topology of the protein .. Can this be done using gromacs and how ?? Regards -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/c1c1ccc7/attachment-0001.html -- 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] RE: simulation of a metal binding sites
Thankx for the reply ... Can you refer some papers which can be helpful for me to do MD simulation of proteins with ions ... It will be of great help.. I searched the gromacs user list but couldn't get much material.. On Thu, Feb 17, 2011 at 12:32 AM, Ran Friedman ran.fried...@lnu.se wrote: Hi, There are methodological difficulties in simulating multivalent ions together with proteins. Check the mailing list for a discussion and reference. This is not an issue of Gromacs but of dealing with protein-ion interactions using a classical non-polarisable force field. Check the literature. Ran. Message: 3 Date: Wed, 16 Feb 2011 20:14:07 -0800 From: bharat gupta bharat.85.m...@gmail.com Subject: [gmx-users] RE: simulation of a metal binding sites To: Discussion list for GROMACS users gmx-users@gromacs.org Message-ID: aanlktin06ut6+wrfpz4a79fq9g-galmk35uxecph+...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi, I have incorporated some metal binding sites(zinc ion) in my protein. Now I want to see whether that region binds to zinc ions or not and what is the effect of ion binding to the topology of the protein .. Can this be done using gromacs and how ?? Regards -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/c1c1ccc7/attachment-0001.html -- 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 -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- 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] RE: simulation of a metal binding sites
bharat gupta wrote: Thankx for the reply ... Can you refer some papers which can be helpful for me to do MD simulation of proteins with ions ... It will be of great help.. I searched the gromacs user list but couldn't get much material.. This list and its users should not supplant your own literature searching and learning experience. A simple Google search for: molecular dynamics metal binding yields over 60,000 results. Doubtless some of these will be useful in getting you started. There are, of course, more sophisticated literature searching tools that might serve you even better. -Justin On Thu, Feb 17, 2011 at 12:32 AM, Ran Friedman ran.fried...@lnu.se mailto:ran.fried...@lnu.se wrote: Hi, There are methodological difficulties in simulating multivalent ions together with proteins. Check the mailing list for a discussion and reference. This is not an issue of Gromacs but of dealing with protein-ion interactions using a classical non-polarisable force field. Check the literature. Ran. Message: 3 Date: Wed, 16 Feb 2011 20:14:07 -0800 From: bharat gupta bharat.85.m...@gmail.com mailto:bharat.85.m...@gmail.com Subject: [gmx-users] RE: simulation of a metal binding sites To: Discussion list for GROMACS users gmx-users@gromacs.org mailto:gmx-users@gromacs.org Message-ID: aanlktin06ut6+wrfpz4a79fq9g-galmk35uxecph+...@mail.gmail.com mailto:aanlktin06ut6%2bwrfpz4a79fq9g-galmk35uxecph%2b...@mail.gmail.com Content-Type: text/plain; charset=iso-8859-1 Hi, I have incorporated some metal binding sites(zinc ion) in my protein. Now I want to see whether that region binds to zinc ions or not and what is the effect of ion binding to the topology of the protein .. Can this be done using gromacs and how ?? Regards -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- next part -- An HTML attachment was scrubbed... URL: http://lists.gromacs.org/pipermail/gmx-users/attachments/20110216/c1c1ccc7/attachment-0001.html -- 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 -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com mailto:monu46...@yahoo.com -- 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] RE: simulation of a metal binding sites
Hi, As mentioned by others, there's really lots of literature out there. I thought I mention a recent study we carried out, because it actually helped discover some new ion binding sites based on MD. By re-examining crystal structures based on these results, we could even find experimental evidence for those ions being there. [1] But actually you didn't tell us which ions you want to simulate? Monovalent ions should be sort of ok, although there are differences among the forcefields (some original KCl used to crystallize). Di-valent ions, in particular Ca2+, are much more tricky. Higher charged ones are a nightmare. The higher the charge, the more likely you might want things like polarization in your simulation. There are also some specific forcefields finely parameterized for ions based on quantum mechanics. I suggest you check out SIBFA [2] by Gresh and Piquemal. Good luck, Marc [1] How Cations Can Assist DNase I in DNA Binding and Hydrolysis http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001000 [2] SIBFA (Sum of Interactions Between Fragments Ab initio computed) http://www.lct.jussieu.fr/pagesperso/jpp/SIBFA.html bharat.85.m...@gmail.com said: Thankx for the reply ... Can you refer some papers which can be helpful for me to do MD simulation of proteins with ions ... It will be of great help.. I searched the gromacs user list but couldn't get much material.. -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baa...@smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 -- 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] RE: simulation of a metal binding sites
Thanks for these two references ... I am trying to simulate a zinc ion (Zn++) binding domains .. Actually the study involves grafting the Zinc ion domain onto some other protein to check whether it binds to ions or not and what will be the effect of ion binding onto the topology of the other protein to which the zinc ion binding domain is attached . On Thu, Feb 17, 2011 at 11:15 PM, Marc Baaden baa...@smplinux.de wrote: Hi, As mentioned by others, there's really lots of literature out there. I thought I mention a recent study we carried out, because it actually helped discover some new ion binding sites based on MD. By re-examining crystal structures based on these results, we could even find experimental evidence for those ions being there. [1] But actually you didn't tell us which ions you want to simulate? Monovalent ions should be sort of ok, although there are differences among the forcefields (some original KCl used to crystallize). Di-valent ions, in particular Ca2+, are much more tricky. Higher charged ones are a nightmare. The higher the charge, the more likely you might want things like polarization in your simulation. There are also some specific forcefields finely parameterized for ions based on quantum mechanics. I suggest you check out SIBFA [2] by Gresh and Piquemal. Good luck, Marc [1] How Cations Can Assist DNase I in DNA Binding and Hydrolysis http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001000 [2] SIBFA (Sum of Interactions Between Fragments Ab initio computed) http://www.lct.jussieu.fr/pagesperso/jpp/SIBFA.html bharat.85.m...@gmail.com said: Thankx for the reply ... Can you refer some papers which can be helpful for me to do MD simulation of proteins with ions ... It will be of great help.. I searched the gromacs user list but couldn't get much material.. -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:baa...@smplinux.de - http://www.baaden.ibpc.fr FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217 -- 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 -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- 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] RE: simulation of a metal binding sites
Hi, I have incorporated some metal binding sites(zinc ion) in my protein. Now I want to see whether that region binds to zinc ions or not and what is the effect of ion binding to the topology of the protein .. Can this be done using gromacs and how ?? Regards -- Bharat Ph.D. Candidate Room No. : 7202A, 2nd Floor Biomolecular Engineering Laboratory Division of Chemical Engineering and Polymer Science Pusan National University Busan -609735 South Korea Lab phone no. - +82-51-510-3680, +82-51-583-8343 Mobile no. - 010-5818-3680 E-mail : monu46...@yahoo.com -- 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
