[gmx-users] Chloroform (CHCl3) solvent box for G53a5 force field
Hi all, I'm trying to simulate a small molecule in a chloroform box using the GROMOS G53a5 forcefield. I realized that the parameters for the solvent are present in the ffG53a5.rtp file, however I could not find a CHCl3 solvent box included in GROMACS. I did find, however, a CHCl3 solvent box equilibrated by PeiQuan Chen (http://lists.gromacs.org/pipermail/gmx-users/2003-May/005572.html) at http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies . I also saw mention of a box for the Amber forcefield, that is now included in AmberTools (amber10/dat/solvents/cform/cform.pdb and chcl3_equil.pdb.1). I took this one and I'm equilibrating it to use it later. In the mean time, I wanted to know if I overlooked something, and there is a CHCl3 box to use with the GROMOS forcefield? Thanks! -- Pablo Englebienne, PhD Institute of Complex Molecular Systems (ICMS) Eindhoven University of Technology, TU/e PO Box 513, HG -1.26 5600 MB Eindhoven, The Netherlands Tel +31 40 247 5349 ___ 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] Chloroform (CHCl3) solvent box for G53a5 force field
Pablo Englebienne wrote: Hi all, I'm trying to simulate a small molecule in a chloroform box using the GROMOS G53a5 forcefield. I realized that the parameters for the solvent are present in the ffG53a5.rtp file, however I could not find a CHCl3 solvent box included in GROMACS. I did find, however, a CHCl3 solvent box equilibrated by PeiQuan Chen (http://lists.gromacs.org/pipermail/gmx-users/2003-May/005572.html) at http://www.gromacs.org/index.php?title=Download_%26_Installation/User_contributions/Molecule_topologies . I also saw mention of a box for the Amber forcefield, that is now included in AmberTools (amber10/dat/solvents/cform/cform.pdb and chcl3_equil.pdb.1). I took this one and I'm equilibrating it to use it later. In the mean time, I wanted to know if I overlooked something, and there is a CHCl3 box to use with the GROMOS forcefield? Not one that is officially distributed. If it was, it would be the /share/gromacs/top subdirectory with other solvent topologies and structures. Probably your best bet is to use the one in the User Contributions section, unless you feel the need to create your own and start from scratch. -Justin Thanks! -- 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://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
