On Sat, Apr 13, 2013 at 4:57 AM, swati rana <[email protected]> wrote:
> Hi, > > I am facing this issue with the energy minimization. The following is the > output when i try to pack the lipids around the protein: > > Steepest Descents: > Tolerance (Fmax) = 1.00000e+01 > Number of steps = 20000 > Step= 14, Dmax= 1.2e-06 nm, Epot= 3.37981e+20 Fmax= inf, atom= > 147 > Energy minimization has stopped, but the forces havenot converged to the > requested precision Fmax < 10 (whichmay not be possible for your system). > It > stoppedbecause the algorithm tried to make a new step whose sizewas too > small, or there was no change in the energy sincelast step. Either way, we > regard the minimization asconverged to within the available machine > precision,given your starting configuration and EM parameters. > > i know this is not an error but the potential energy is very high i went > through the mailing list as well but could not get the answer for my > question. > > THERE IS AN OVERLAP IN POPC AND LIGAND. WHEN I SELECT MY LIGAND IN PYMOL > simultaneously ONE POPC ATOM ALSO GETS SELECTED and i understand that is > the problem but what should be done to correct this. i tried to reposition > the ligand and copied its coordinates in the last that worked in system.gro > file but again when system_inflated.gro file was generated again there was > an overlap. please tell how to solve this issue. how to correct this > overlap thing. Do i have to number each atom from the start to end in a > flow like instead of popc 1st molecule to be numbered as 1 should i > renumber it to what was the last for proteins. > > I don't know if InflateGRO is even capable of dealing with ligands. Try the workflow without it to make sure it works for a simple system of protein and lipids. Then try again with the ligand included. If the latter fails, then it's simply a limitation in InflateGRO. In that case, you'll have to build the protein-lipid system completely and then figure out some way to insert the ligand. Numbering should not be an issue at all; positions are the problem here. -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
