[gmx-users] problem with FeS cluster
Hello user Can anybody please tell me how to prepare a topology file for the FES4 cluster incorporated in a protein Subarna Cricket on your mind? Visit the ultimate cricket website. Enter http://beta.cricket.yahoo.com___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with FeS cluster
subarna thakur wrote: Hello user Can anybody please tell me how to prepare a topology file for the FES4 cluster incorporated in a protein I passed along some useful information to you yesterday. There is no easy answer. To do so would involve a large amount of work, in any case, if it is even possible to model this species using a standard MM force field. -Justin Subarna Cricket on your mind? Visit the ultimate cricket website. Enter now! http://in.rd.yahoo.com/tagline_cricket_1/*http://beta.cricket.yahoo.com ___ 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 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://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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with FeS cluster
Hi I have gone through the material you have earlier mentioned but I am still in dark and not sure where to start. Should I make chages in the relevent .rtp file to incorporate the atoms of the FE-S cluster? Subarna From: Justin A. Lemkul jalem...@vt.edu To: Discussion list for GROMACS users gmx-us...@gromacs..org Sent: Wednesday, 3 June, 2009 4:46:37 PM Subject: Re: [gmx-users] problem with FeS cluster subarna thakur wrote: Hello user Can anybody please tell me how to prepare a topology file for the FES4 cluster incorporated in a protein I passed along some useful information to you yesterday. There is no easy answer. To do so would involve a large amount of work, in any case, if it is even possible to model this species using a standard MM force field. -Justin Subarna Cricket on your mind? Visit the ultimate cricket website. Enter now! http://in.rd.yahoo.com/tagline_cricket_1/*http://beta.cricket.yahoo..com ___ 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 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 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Own a website.Get an unlimited package.Pay next to nothing.*Go to http://in.business.yahoo.com/___ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] problem with FeS cluster
subarna thakur wrote: Hi I have gone through the material you have earlier mentioned but I am still in dark and not sure where to start. Should I make chages in the relevent .rtp file to incorporate the atoms of the FE-S cluster? If you derive your own parameters, you can either make an .rtp entry for the cluster, or simply generate an .itp file by hand. Either way will work, but no matter what, it is not a trivial task to derive the appropriate parameters. Making and .rtp entry/.itp file is simple, proving the validity of your parameters is not. -Justin Subarna *From:* Justin A. Lemkul jalem...@vt.edu *To:* Discussion list for GROMACS users gmx-users@gromacs.org *Sent:* Wednesday, 3 June, 2009 4:46:37 PM *Subject:* Re: [gmx-users] problem with FeS cluster subarna thakur wrote: Hello user Can anybody please tell me how to prepare a topology file for the FES4 cluster incorporated in a protein I passed along some useful information to you yesterday. There is no easy answer. To do so would involve a large amount of work, in any case, if it is even possible to model this species using a standard MM force field. -Justin Subarna Cricket on your mind? Visit the ultimate cricket website. Enter now! http://in.rd.yahoo.com/tagline_cricket_1/*http://beta.cricket.yahoo.com ___ gmx-users mailing listgmx-users@gromacs.org mailto: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 gmx-users-requ...@gromacs.org mailto: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 mailto: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 gmx-users-requ...@gromacs.org mailto:gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php Bollywood news, movie reviews, film trailers and more! Click here. http://in.rd.yahoo.com/tagline_movies_1/*http://in.movies.yahoo.com/?wm=n/ -- 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://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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
