I've no idea what the real limitation in InflateGRO might be, but if it is based on the [moleculetype], then a combined protein+ligand [moleculetype] might be effectlve.
Mark On Sat, Apr 13, 2013 at 2:38 PM, Justin Lemkul <[email protected]> wrote: > 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 > -- 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
