On Mon, Nov 30, 2009 at 8:18 PM, Justin A. Lemkul <[email protected]> wrote: > > > Francesco Pietra wrote: >> >> Failed to specify that both the DPPC bilayer and the box of water are >> from equilibrated systems in MARTIN web, while the protein was Amber >> minimized (and MD) before generating the CG. >> >> I have tried the cg protein alone >> >> genbox -cp my.pdb -box 15 -o my.gro >> > > Again I ask why you are using SPC as the solvent. If you indeed want to use > the MARTINI CG water representation, you must pass its configuration > explicitly to the -cs flag. Otherwise, the default (spc216.gro) is used.
The water that I set around the extracellular part of the protein was equilibrated cg water (by just multiplying the box furnished on MARTINI). In relation to the command above, I don't understand your remark, simply because there is no water at all, both in the input .pdb and output.gro. This is true for my previous post, too. > > Are you defining the protein's position in the box before solvation? Using > editconf -c is your friend. I did present work before getting your mail. Curiously, gmail now places your mail in spam. Luckily I noticed that. A point I have to pay much attention to - for a possible major mistake in my procedure - is your "before solvation". I assumed no solvation at all. > >> grompp -f em.mdp -c my.gro -p my.top -o topol.tpr >> >> mdrun -v -s topol.tpr >> >> steepest descents converged to machine precision but not to the >> requested Fmax < 2000 >> >> Pot Ener 7.1e+08 >> Max force 6.1e+10 on atom 983 >> Norm of force 2.5e+11 >> >> confout.gro shows that one of the subunits has been displaced from the >> multimer (apparently both intact) There is a long bond between the >> displaced subunit and the rest of the multimer, very closely to the >> atom 983 of max force, located in the pore region. I have scarce >> experience with gromacs yet, hope that this suggests remedies. I used >> a crude version of em.mdp. >> > > Well, there are several potential problems. One is the box size (as I > mentioned in my last message). The other question is whether or not the > conversion from atomistic to CG was done correctly. I know I have mentioned > the problems with the MARTINI script a number of times, and perhaps this has > also come up in our discussions before, but do check that the starting CG > coordinates make sense. The cg protein model superimposes nicely to the full-atom model. The dimensions I gave in my previous mail were DPPC and W inclusive but "-box 15" is still to small. The protein might have seen its neighbor. > > Beyond that, try an in vacuo minimization of your protein and see what > happens there. Do you mean without setting "-box"? I got confused about that, I thought to have vacum around the protein (or the protein+DPPC+W of previous mail) with genbox -cp my.pdb -box 15 -o my.gro I'll try tomorrow to implement all your suggestions. Thanks a lot francesco > > -Justin > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://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/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/mailing_lists/users.php > > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php
