Re: [gmx-users] Fwd: How can I do the simulation of a protein with Tyr (SO3H)
fulya caglar wrote: Hi Tsjerk, Thanks for your help.You're right about taking paths well walked by others,before starting new trails but I have to do this simulation for my study:( Then do it in a right way. Hurry up! Thanks very much for your suggestions again. Sincerely Fulya */Tsjerk Wassenaar [EMAIL PROTECTED]/* wrote: Hi Fulya, In addition to Mark's comments, if you have a friend who has the proper background for such parameterization he/she will know what to do and I don't need to describe the process. The basic thing is that if you're a novice with MD, it's best to first take the paths well walked by others, before starting new trails (in terms of methodology/parameters; I don't want to suggest to repeat projects from others, that's basically what tutorials are for, but I would advice to use proteins/dna with no strings attached). Regarding the mail server, the first two mails only arrived as forwarded mails, with a lot of junk around the main question (which makes reading less convenient). Best, Tsjerk On 3/28/07, Mark Abraham wrote: fulya caglar wrote: Hi Tsjerk, Do you know how can I add parameters for sulfite bound?You are right I have little experience in this field but maybe one of my friends can do this.I would be very grateful if you can explain parameterization briefly. It's an involved process, which varies considerably depending on the force field you're trying to extend. You should start by reading the paper that describes the parameterization of the force field you're trying to extend, and then thinking hard about how you can follow a similar process to get parameters that are consistent. Mark ___ gmx-users mailing list gmx-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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing list gmx-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 We won't tell. Get more on shows you hate to love http://us.rd.yahoo.com/evt=49980/*http://tv.yahoo.com/collections/265 (and love to hate): Yahoo! TV's Guilty Pleasures list. http://us.rd.yahoo.com/evt=49980/*http://tv.yahoo.com/collections/265 ___ 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 ___ 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] Fwd: How can I do the simulation of a protein with Tyr (SO3H)
Hi Fulya, In addition to Mark's comments, if you have a friend who has the proper background for such parameterization he/she will know what to do and I don't need to describe the process. The basic thing is that if you're a novice with MD, it's best to first take the paths well walked by others, before starting new trails (in terms of methodology/parameters; I don't want to suggest to repeat projects from others, that's basically what tutorials are for, but I would advice to use proteins/dna with no strings attached). Regarding the mail server, the first two mails only arrived as forwarded mails, with a lot of junk around the main question (which makes reading less convenient). Best, Tsjerk On 3/28/07, Mark Abraham [EMAIL PROTECTED] wrote: fulya caglar wrote: Hi Tsjerk, Do you know how can I add parameters for sulfite bound?You are right I have little experience in this field but maybe one of my friends can do this.I would be very grateful if you can explain parameterization briefly. It's an involved process, which varies considerably depending on the force field you're trying to extend. You should start by reading the paper that describes the parameterization of the force field you're trying to extend, and then thinking hard about how you can follow a similar process to get parameters that are consistent. Mark ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] Fwd: How can I do the simulation of a protein with Tyr (SO3H)
Hi Tsjerk, Thanks for your help.You're right about taking paths well walked by others,before starting new trails but I have to do this simulation for my study:( Thanks very much for your suggestions again. Sincerely Fulya Tsjerk Wassenaar [EMAIL PROTECTED] wrote: Hi Fulya, In addition to Mark's comments, if you have a friend who has the proper background for such parameterization he/she will know what to do and I don't need to describe the process. The basic thing is that if you're a novice with MD, it's best to first take the paths well walked by others, before starting new trails (in terms of methodology/parameters; I don't want to suggest to repeat projects from others, that's basically what tutorials are for, but I would advice to use proteins/dna with no strings attached). Regarding the mail server, the first two mails only arrived as forwarded mails, with a lot of junk around the main question (which makes reading less convenient). Best, Tsjerk On 3/28/07, Mark Abraham wrote: fulya caglar wrote: Hi Tsjerk, Do you know how can I add parameters for sulfite bound?You are right I have little experience in this field but maybe one of my friends can do this.I would be very grateful if you can explain parameterization briefly. It's an involved process, which varies considerably depending on the force field you're trying to extend. You should start by reading the paper that describes the parameterization of the force field you're trying to extend, and then thinking hard about how you can follow a similar process to get parameters that are consistent. Mark ___ gmx-users mailing list gmx-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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing list gmx-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 - We won't tell. Get more on shows you hate to love (and love to hate): Yahoo! TV's Guilty Pleasures list.___ 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] Fwd: How can I do the simulation of a protein with Tyr (SO3H)
fulya caglar wrote: Hi Tsjerk, Thanks for your help.You're right about taking paths well walked by others,before starting new trails but I have to do this simulation for my study:( If whoever set this problem didn't understand this problem with sulfite parameters, then they've set a poor problem for a person new to MD. That implies a poor knowledge of MD and of people. Perhaps you should renegotiate your problem, or choose a new setter :-) Mark ___ 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] Fwd: How can I do the simulation of a protein with Tyr (SO3H)
Hi Fulya, I can understand this. But if the person who issued this assignment thought it was something to do in an afternoon he/she was quite mistaken. Now, it is still possible to do it, but it depends on how much time you have. Plenty of people have once started with parameterization. None of us was born with knowledge of it (as far as I know). But it does mean that you first have to make sure that you understand molecular dynamics. You have to understand the (role of) the force field and the philosophies behind force fields. You'll have to choose a force field which you think fits best with what you want to do. Then you'll have to get to understand the conditions for that particular force field; usually there is a strict interplay between a force field and simulation parameters, notably the treatment of electrostatic interactions, the cut-off range and the water model. You'll have to find a study describing the parameterization of a molecule for that force field and replicate it, to see if you can reproduce the results and then you're probably ready to try to tackle your molecule. Now, sulfite bound tyrosine is not merely a coupling between a well-parameterized tyrosine residue and a well-parameterized sulfite group. Tyrosine and sulfite are both conjugated systems, which is well fun if you bind them together. That will change the whole charge distribution on both. That being said.., have you already checked for a description of sulfite tyrosine in the literature? That would save you a good deal of trouble. Otherwise you'll have to convince your supervisor to allow you more time. Good luck, Tsjerk On 3/29/07, Mark Abraham [EMAIL PROTECTED] wrote: fulya caglar wrote: Hi Tsjerk, Thanks for your help.You're right about taking paths well walked by others,before starting new trails but I have to do this simulation for my study:( If whoever set this problem didn't understand this problem with sulfite parameters, then they've set a poor problem for a person new to MD. That implies a poor knowledge of MD and of people. Perhaps you should renegotiate your problem, or choose a new setter :-) Mark ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] Fwd: How can I do the simulation of a protein with Tyr (SO3H)
Hi Fulya, You can't just simulate everything you set your mind on. There are no parameters for sulfite bound tyrosine in the database (just what it says). You have to add them yourself, which I don't recommend at this point, since it is clear you have but little experience in this field (and parameterization is an advanced topic). By the way, do you have some problems with the mail server? Best, Tsjerk On 3/27/07, fulya caglar [EMAIL PROTECTED] wrote: Note: forwarded message attached. Bored stiff? Loosen up... Download and play hundreds of games for free on Yahoo! Games. -- Forwarded message -- From: fulya caglar [EMAIL PROTECTED] To: Gromacs [EMAIL PROTECTED] Date: Tue, 27 Mar 2007 04:45:43 -0700 (PDT) Subject: How can I do the simulation of a protein with Tyr (SO3H) Hi! I'm trying to do a simulation of a protein with bound sulfite ion (Tyr (SO3H)).After the first command ( pdb2gmx) I am getting the following error message : - Fatal error: Residue 'SUL' not found in residue topology database - I would be very glad to know why I get this type of error and what can I do about this. With thanks Sincerely Fulya TV dinner still cooling? Check out Tonight's Picks on Yahoo! TV. ___ 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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ 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] Fwd: How can I do the simulation of a protein with Tyr (SO3H)
Hi Tsjerk, Do you know how can I add parameters for sulfite bound?You are right I have little experience in this field but maybe one of my friends can do this.I would be very grateful if you can explain parameterization briefly. And I dont think there is a problem with the mail server?Why did you ask? Thank you very much!!! Sincerly Fulya - From: Tsjerk Wassenaar [EMAIL PROTECTED] To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: Re: [gmx-users] Fwd: How can I do the simulation of a protein with Tyr (SO3H) Hi Fulya, You can't just simulate everything you set your mind on. There are no parameters for sulfite bound tyrosine in the database (just what it says). You have to add them yourself, which I don't recommend at this point, since it is clear you have but little experience in this field (and parameterization is an advanced topic). By the way, do you have some problems with the mail server? Best, Tsjerk On 3/27/07, fulya caglar wrote: Note: forwarded message attached. Bored stiff? Loosen up... Download and play hundreds of games for free on Yahoo! Games. -- Forwarded message -- From: fulya caglar To: Gromacs Date: Tue, 27 Mar 2007 04:45:43 -0700 (PDT) Subject: How can I do the simulation of a protein with Tyr (SO3H) Hi! I'm trying to do a simulation of a protein with bound sulfite ion (Tyr (SO3H)).After the first command ( pdb2gmx) I am getting the following error message : - Fatal error: Residue 'SUL' not found in residue topology database - I would be very glad to know why I get this type of error and what can I do about this. With thanks Sincerely Fulya TV dinner still cooling? Check out Tonight's Picks on Yahoo! TV. ___ gmx-users mailing list gmx-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 -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing list gmx-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 - Don't be flakey. Get Yahoo! Mail for Mobile and always stay connected to friends.___ 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] Fwd: How can I do the simulation of a protein with Tyr (SO3H)
fulya caglar wrote: Hi Tsjerk, Do you know how can I add parameters for sulfite bound?You are right I have little experience in this field but maybe one of my friends can do this.I would be very grateful if you can explain parameterization briefly. It's an involved process, which varies considerably depending on the force field you're trying to extend. You should start by reading the paper that describes the parameterization of the force field you're trying to extend, and then thinking hard about how you can follow a similar process to get parameters that are consistent. Mark ___ 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
