I got into this part of the KALP-15 in DPPC tutorial "Note how many lipids were deleted and update the [ molecules ] directive of your topology accordingly. Run energy minimization. Then, scale down the lipids by a factor of 0.95 (assuming you have used default names, the result of the minimization is called "confout.gro"):
perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat Follow this up by another round of EM. During the "shrinking" steps, be sure to change the cutoff value to 0, or else you will continue to delete lipids! After 26 iterations of scaling down by 0.95, I reached an area per lipid of ~71 Å2, above the experimental value of ~62 Å2. Since the script tends to overestimate the area per lipid, this value is good enough to continue to equilibration." I added the line at the topol.top [molecule] DDPC 126 Then I tried grompp -f minim.mdp -c system_inflate.gro -p topol.top -o em.tpr -maxwarn 1 Somehow, it worked. But I didn't get any confout.gro file so the perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat doesn't work. Melsa Rose Ducut > On Jan 25, 2014, at 12:41 PM, "Justin Lemkul [via GROMACS]" > <[email protected]> wrote: > > > > On 1/24/14, 11:21 PM, jhosamelly wrote: > > > > > Thanks Justin. I fixed the problem earlier but when I got to > > > > "2. Pack the lipids around the protein > > > > The easiest method I have found so far for packing lipids around an > > embedded > > protein is the InflateGRO methodology (ref), available here. First, > > concatenate the protein and bilayer structure files: > > > > cat KALP_newbox.gro dppc128_whole.gro > system.gro > > > > Remove unnecessary lines (the box vectors from the KALP structure, the > > header information from the DPPC structure) and update the second line of > > the coordinate file (total number of atoms) accordingly." > > > > I don't know what file to edit. Remove unnecessary lines in what file? > > In system.gro. If you study the file format and examine what you have > created, > you will see that there is extraneous stuff that will break the file format. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > [hidden email] | (410) 706-7441 > > ================================================== > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to [hidden email]. > > > If you reply to this email, your message will be added to the discussion > below: > http://gromacs.5086.x6.nabble.com/Question-Re-KALP-15-in-DPPC-tutorial-tp5014033p5014038.html > To unsubscribe from Question Re. KALP-15 in DPPC tutorial, click here. > NAML -- View this message in context: http://gromacs.5086.x6.nabble.com/Question-Re-KALP-15-in-DPPC-tutorial-tp5014033p5014042.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to [email protected].
