Re: [gmx-users] Applying an improper to S-S bond
DimitryASuplatov wrote: Hello, The question is not actually about S-S. I have a covalent bond between Cys (SG atom) ang Tyr (CE atom) residues. I`ve corrected the specbonds.dat and oplsaa topology to create a new residue (tyr2) and I use cys2 topology for cystein. During the MD the this covalent bond rotates a lot, so I think of applying an improper to the bond. The problem is that the fourth atom of a dihedral is always in another residue, I mean that I need the TYR2 CE atom to be present in CYS2 topology to set the improper and this is obviously impossible. 1/ How can I apply improper for this case? Read and understand the relevant bits of chapters 4 & 5 of the manual, and add some suitable function to the .top file by hand. 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Applying an improper to S-S bond
DimitryASuplatov wrote: Hello, The question is not actually about S-S. I have a covalent bond between Cys (SG atom) ang Tyr (CE atom) residues. I`ve corrected the specbonds.dat and oplsaa topology to create a new residue (tyr2) and I use cys2 topology for cystein. During the MD the this covalent bond rotates a lot, so I think of applying an improper to the bond. The problem is that the fourth atom of a dihedral is always in another residue, I mean that I need the TYR2 CE atom to be present in CYS2 topology to set the improper and this is obviously impossible. 1/ How can I apply improper for this case? 2/ Any other (simpler) ways to freez the rotation? Probably a dihedral restraint is more appropriate. -Justin Thanks ___ 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 Graduate Research Assistant 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
[gmx-users] Applying an improper to S-S bond
Hello, The question is not actually about S-S. I have a covalent bond between Cys (SG atom) ang Tyr (CE atom) residues. I`ve corrected the specbonds.dat and oplsaa topology to create a new residue (tyr2) and I use cys2 topology for cystein. During the MD the this covalent bond rotates a lot, so I think of applying an improper to the bond. The problem is that the fourth atom of a dihedral is always in another residue, I mean that I need the TYR2 CE atom to be present in CYS2 topology to set the improper and this is obviously impossible. 1/ How can I apply improper for this case? 2/ Any other (simpler) ways to freez the rotation? Thanks ___ 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
