[gmx-users] Parameterization of a molecule containing a radical (oxygen)

hough. If this parameterization is impossible to do we will give up, but we would like to be sure about it. Thanks in advance for any answer you could provide. <http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=137994&loc=ec_rcs> -- Simone Cirri -- gmx-users mailing listgm

[gmx-users] Protein in water/DMSO mixture with Amber

Hi all, to say the truth I already sent a message regarding this subject some months ago, but since so much time has passed I thought I'd open a new thread, also because the situation has quite evolved. I'm trying to set up a simulation of a small (62 residues) protein in a mixture of water and DM

[gmx-users] Converting a solvent box file from Amber

e understand how to do it considering that "protonate" seems to be forcefield-dependent (dependent from Gromos, of course). Thanks a lot Simone Cirri -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://ww

Re: [gmx-users] Water molecule starting at atom X can not be settled; can't find a solution

ic tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 Thank you Simone Cirri ___ gmx-users mailing li

[gmx-users] Water molecule starting at atom X can not be settled; can't find a solution

= 300.0 gen_seed= 173529 I really don't know what else I could do... if someone has an idea, I would be glad to hear it. Thank you Simone Cirri PhD student at the Structural Biology Lab of University of Siena, Italy ___ gmx-users ma

[gmx-users] Re: Simulation of a protein in a water/DMSO box

Justin A. Lemkul wrote: Simone Cirri wrote: > > Hi everyone, > > I need to run a simulation of a protein in a water/DMSO mixture. I can't > quite understand how should I do this... should I normally solvate the > protein with water and then replace a certain number of water

[gmx-users] Simulation of a protein in a water/DMSO box

this case, how should I do it? Is there a way of replacing solvent molecules with other solvent molecules, but of a different type? I'm sorry but I don't know which procedure to follow. Thanks in advance Simone Cirri simoneci...@gmail.com __