[gmx-users] FeS cluster
Hello We dont have the parameters for Fe4S4 cluster in any of the the gomacs force fields but if we able to make the .itp file for the cluster manually with the help of Quantum mechanical calculations, can we place the .itp file of fe4s4 in the include section of the protein .top file later as done in the case of drug/enzyme tutorial of gromacs.Can we fellow the steps given in the tutorial for the Fe4S4 cluster? With regards Subarna Love Cricket? Check out live scores, photos, video highlights and more. Click here http://cricket.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/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] FeS cluster
subarna thakur wrote: Hello We dont have the parameters for Fe4S4 cluster in any of the the gomacs force fields but if we able to make the .itp file for the cluster manually with the help of Quantum mechanical calculations, can we place the .itp file of fe4s4 in the include section of the protein .top file later as done in the case of drug/enzyme tutorial of gromacs.Can we fellow the steps given in the tutorial for the Fe4S4 cluster? Yes and no. Even if you are able to obtain suitable parameters (which will be difficult at best), if there are bonded interactions to the cluster, then you will have to make a composite topology - i.e. a single [ moleculetype ]. Depending on the geometry and sequence order of your two chains, that might be painful too. Frankly, this project would be a very poor one for a first effort at MD. Get some experience with GROMACS doing something more straightforward, learning to walk, before trying to run juggling razors. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
[gmx-users] Fes cluster
Hello The protein I am considering is a homodimer with two chains with a Fe4S4 cluster situated at the interface of two chains with connections with both the chains by cystein residues.I have generated the .itp file of the Fe4S4 cluster and .top of the protein with pdb2gmx command.The .top file is like this- -; ; File '1braf.top' was generated ; By user: root (0) ; On host: localhost.localdomain ; At date: Mon Jul 27 13:12:40 2009 ; ; This is your topology file ; I Have a Bad Case Of Purple Diarrhea (Urban Dance Squad) ; ; Include forcefield parameters #include ffoplsaa.itp ; Include chain topologies #include 1braf_A.itp #include 1braf_B.itp ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_A 1 Protein_B 1 - I want to know how do I include the Fe4S4 .itp file in the topology file of the protein and How do I include the connect information of the protein and FES cluster. Regards Subarna Yahoo! recommends that you upgrade to the new and safer Internet Explorer 8. http://downloads.yahoo.com/in/internetexplorer/___ gmx-users mailing listgmx-users@gromacs.org http://lists.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] Fes cluster
subarna thakur wrote: Hello The protein I am considering is a homodimer with two chains with a Fe4S4 cluster situated at the interface of two chains with connections with both the chains by cystein residues.I have generated the .itp file of the Fe4S4 cluster and .top of the protein with pdb2gmx command.The .top file is like this- -; ; File '1braf.top' was generated ; By user: root (0) ; On host: localhost.localdomain ; At date: Mon Jul 27 13:12:40 2009 ; ; This is your topology file ; I Have a Bad Case Of Purple Diarrhea (Urban Dance Squad) ; ; Include forcefield parameters #include ffoplsaa.itp ; Include chain topologies #include 1braf_A.itp #include 1braf_B.itp ; Include water topology #include spc.itp #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include generic topology for ions #include ions.itp [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_A 1 Protein_B 1 - I want to know how do I include the Fe4S4 .itp file in the topology file of the protein Do you have one? Does your force field have suitable parameters for this moiety? and How do I include the connect information of the protein and FES cluster. You will need to understand parts of chapter 5 of the manual thoroughly. Work on understanding a simple diglycine .top file first. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://lists.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
