[gmx-users] g_lie question

I am trying to figure out how to use the g_lie tool in gromacs. I have the dGbind value for the ligand-solvent interactions and for the protein-ligand complex. However, I cannot find in the manual what units these values are. I get the following: DGbind = 1953867.080 (0.664) and DGbind =

[gmx-users] Re: g_lie question

I see from the file that the units are in KJ/mol, which means my calculations are really off. But regardless, I still don't understand what the value in parentheses means, like (nan). If anyone can decipher, please respond. Thank you for your time. 2egy On Nov 18, 2011, at 11:43 AM, EGY wrote

Re: [gmx-users] Small molecule - CHARMM

I'm not a regular contributor, but I thought I'd comment since I just went through this exercise. I found the tutorial from the VMD group to be the easiest to follow. http://www.ks.uiuc.edu/Training/SumSchool/materials/sources/tutorials/05-qm-tutorial/part1.html This tutorial uses GAMESS, which

[gmx-users] modeling cation-pi box

. Is there a way to restrain the cation portion of the small molecule to within the aromatic box? Or is there a better forcefield, which will take these interactions into consideration. Thanks. Egy-- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please

Re: [gmx-users] modeling cation-pi box

the simulations. Is it possible to enhance these interactions, since there is no defined force constants that describes these interactions? Thanks. Egy On Oct 24, 2011, at 12:19 PM, Justin A. Lemkul wrote: EGY wrote: I am interesting in modeling a small molecule ligand-protein complex