Re: [gmx-users] interaction between ligand and protein
Dear Mahboobeh, You mean from which frame you should choose? If so, first look at RMSD values in order to make sure your system is stable. If it is stable you can choose the last configuration. Best, Onur On 30 Nov 2014, at 18:57, Mahboobeh Eslami mahboobeh.esl...@yahoo.com wrote: hi GMX users i have simulated the protein-ligand complex by gromacs for 20ns. Which configuration should be chosen for the study of interactions between proteins and ligands? Thank you for your kindness -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Bu e-posta mesaji kisiye ozel olup, gizli bilgiler iceriyor olabilir. Eger bu e-posta mesaji size yanlislikla ulasmissa, icerigini hicbir sekilde kullanmayiniz ve e-postayi siliniz. Hacettepe Universitesi bu e-posta mesajinin icerigi ile ilgili olarak hicbir hukuksal sorumlulugu kabul etmez. The information contained in this communication may contain confidential or legally privileged information. Hacettepe University doesn't accept any legal responsibility for the contents and attachments of this message. The sender does not accept any liability for any errors or omissions or any viruses in the context of this message which arise as a result of internet transmission. Bu e-posta mesaji kisiye özel olup, gizli bilgiler iceriyor olabilir. Eger bu e-posta mesaji size yanlislikla ulasmissa, icerigini hicbir sekilde kullanmayiniz ve e-postayi siliniz. Hacettepe Universitesi bu e-posta mesajinin icerigi ile ilgili olarak hicbir hukuksal sorumlulugu kabul etmez. The information contained in this communication may contain confidential or legally privileged information. Hacettepe University doesn't accept any legal responsibility for the contents and attachments of this message. The sender does not accept any liability for any errors or omissions or any viruses in the context of this message which arise as a result of internet transmission. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Protein comparison
Dear md, I mean that what kind of analysis I can perform? Should I perform binding energy calculation or rmsd calculation for protein stability change? You can perform binding energy calculation, of course. You have a docked structure. First make sure your docking simulation is reliable. It is important which software you have used and what kind of protein and ligand you have. After making sure your docking result is reliable you have to carry out MD simulation for testing whether your complex structure is stable. From MD simulations you are able to carry out analysis: what kind of interactions you have? Charged groups, Hydrogen bonding etc. After making sure your structure is stable during MD simulation (you can check RMSD values for this) you are able to calculate Potential of Mean Force using Umbrella Sampling or you can perform Free Energy Perturbation calculations. Please explore your structure and make sure your docking result is proper firstly. Best, Onur On 17 Nov 2014, at 13:42, rama david ramadavidgr...@gmail.com wrote: Dear MD, You are asking this question again. but let to tell you, the energy comparison are made by docking software. Please see the manual of software and mentioned the name of software you are using. By gromacs you can do the MD simulation and do analysis of other interaction pattern. You cant compare just docking result in gromacs. On Mon, Nov 17, 2014 at 9:37 AM, md kashif kashifzamir180...@gmail.com mailto:kashifzamir180...@gmail.com wrote: Dear all I have protein pdb file and protein+ligand pdb file generated after docking. How can I compare them by using gromacs? With the word compare I mean that what kind of analysis I can perform? Should I perform binding energy calculation or rmsd calculation for protein stability change? Kindly suggest any tutorial for help. Thanks On Sun, Nov 16, 2014 at 3:13 PM, md kashif kashifzamir180...@gmail.com wrote: Dear all I have protein pdb file and protein+ligand pdb file generated after docking. How can I compare them by using gromacs? Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Bu e-posta mesaji kisiye ozel olup, gizli bilgiler iceriyor olabilir. Eger bu e-posta mesaji size yanlislikla ulasmissa, icerigini hicbir sekilde kullanmayiniz ve e-postayi siliniz. Hacettepe Universitesi bu e-posta mesajinin icerigi ile ilgili olarak hicbir hukuksal sorumlulugu kabul etmez. The information contained in this communication may contain confidential or legally privileged information. Hacettepe University doesn't accept any legal responsibility for the contents and attachments of this message. The sender does not accept any liability for any errors or omissions or any viruses in the context of this message which arise as a result of internet transmission. Bu e-posta mesaji kisiye özel olup, gizli bilgiler iceriyor olabilir. Eger bu e-posta mesaji size yanlislikla ulasmissa, icerigini hicbir sekilde kullanmayiniz ve e-postayi siliniz. Hacettepe Universitesi bu e-posta mesajinin icerigi ile ilgili olarak hicbir hukuksal sorumlulugu kabul etmez. The information contained in this communication may contain confidential or legally privileged information. Hacettepe University doesn't accept any legal responsibility for the contents and attachments of this message. The sender does not accept any liability for any errors or omissions or any viruses in the context of this message which arise as a result of internet transmission. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Protein comparison
Dear kashifzamir, What will you compare? As I guess, if you want to compare the protein structure before and after docking, you have to use VMD. Best Onur On 16 Nov 2014, at 11:43, md kashif kashifzamir180...@gmail.com wrote: Dear all I have protein pdb file and protein+ligand pdb file generated after docking. How can I compare them by using gromacs? Thanks -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Bu e-posta mesaji kisiye ozel olup, gizli bilgiler iceriyor olabilir. Eger bu e-posta mesaji size yanlislikla ulasmissa, icerigini hicbir sekilde kullanmayiniz ve e-postayi siliniz. Hacettepe Universitesi bu e-posta mesajinin icerigi ile ilgili olarak hicbir hukuksal sorumlulugu kabul etmez. The information contained in this communication may contain confidential or legally privileged information. Hacettepe University doesn't accept any legal responsibility for the contents and attachments of this message. The sender does not accept any liability for any errors or omissions or any viruses in the context of this message which arise as a result of internet transmission. Bu e-posta mesaji kisiye özel olup, gizli bilgiler iceriyor olabilir. Eger bu e-posta mesaji size yanlislikla ulasmissa, icerigini hicbir sekilde kullanmayiniz ve e-postayi siliniz. Hacettepe Universitesi bu e-posta mesajinin icerigi ile ilgili olarak hicbir hukuksal sorumlulugu kabul etmez. The information contained in this communication may contain confidential or legally privileged information. Hacettepe University doesn't accept any legal responsibility for the contents and attachments of this message. The sender does not accept any liability for any errors or omissions or any viruses in the context of this message which arise as a result of internet transmission. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] energy minimization
Dear md, I think I understand what you want to say. If you want the energy needed to pull away from the binding site, try using Umbrella Sampling method. You will get Potential of Mean Force which you are able to calculate binding constant directly. Best Onur On 11/14/14 08:52 AM, rama david ramadavidgr...@gmail.com wrote: Dear md, On docking the only change in enegy for ligand takes place. The protein is rigid generally. So what was your condition was it regid or flexible for some residues?? so how it can have the energy the energy of single peptide,single protein and the energy of docking complex is compared. The docking complex is not always has so much less energy. which software u used? read the manual of software that may tell about there way to compare the enrgy and algorithm. what is your aim. what u want to say by analysis?? Please mention all these then only someone can suggest you any opinion. With regards, Rama david On Fri, Nov 14, 2014 at 12:06 AM, Justin Lemkul jalem...@vt.edu wrote: On 11/13/14 2:14 AM, md kashif wrote: Dear all Can anyone suggest that how to compare change in energy of my protein before docking and after docking by a ligand. Please suggest any suitable tutorial or paper if possible. You can easily calculate an energy value for the protein (single point energy calculation), but it's not a free energy and it's totally force field-dependent. Proteins are generally (mostly) rigid during docking, so any change in the energy is probably small. If this is related to your previous posts about the energy value after minimization, it's really not a useful quantity because the systems are simply different. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. Bu e-posta mesaji kisiye ozel olup, gizli bilgiler iceriyor olabilir. Eger bu e-posta mesaji size yanlislikla ulasmissa, icerigini hicbir sekilde kullanmayiniz ve e-postayi siliniz. Hacettepe Universitesi bu e-posta mesajinin icerigi ile ilgili olarak hicbir hukuksal sorumlulugu kabul etmez. The information contained in this communication may contain confidential or legally privileged information. Hacettepe University doesn't accept any legal responsibility for the contents and attachments of this message. The sender does not accept any liability for any errors or omissions or any viruses in the context of this message which arise as a result of internet transmission. Bu e-posta mesaji kisiye ozel olup, gizli bilgiler iceriyor olabilir. Eger bu e-posta mesaji size yanlislikla ulasmissa, icerigini hicbir sekilde kullanmayiniz ve e-postayi siliniz. Hacettepe Universitesi bu e-posta mesajinin icerigi ile ilgili olarak hicbir hukuksal sorumlulugu kabul etmez. The information contained in this communication may contain confidential or legally privileged information. Hacettepe University doesn't accept any legal responsibility for the contents and attachments of this message. The sender does not accept any liability for any errors or omissions or any viruses in the context of this message which arise as a result of internet transmission. Bu e-posta mesaji kisiye özel olup, gizli bilgiler iceriyor olabilir. Eger bu e-posta mesaji size yanlislikla ulasmissa, icerigini hicbir sekilde kullanmayiniz ve e-postayi siliniz. Hacettepe Universitesi bu e-posta mesajinin icerigi ile ilgili olarak hicbir hukuksal sorumlulugu kabul etmez. The information contained in this communication may contain confidential or legally privileged information. Hacettepe University doesn't accept any legal responsibility for the contents and attachments of this message. The sender does not accept any liability for any errors or omissions or any viruses in the context of this message which
