[gmx-users] mdrun error

Sun Nov 11 05:11:25 CET 2007

Hi justin 
I placed POPC membrane in a box too of same dimension as the box of alamethicin and centred it too so that alamethicin is placed correctly in the membrane. 
I am attaching the pdb please have a look.Any help would be appreciated

Pragya

> Date: Sat, 10 Nov 2007 12:42:01 -0500> From: jalemkul at vt.edu> To: gmx-users at gromacs.org> Subject: RE: [gmx-users] mdrun error> > Quoting pragya chohan <pragyachohan at hotmail.com>:> > > Thanks Justin for your reply. I am generating the starting structure through> > genbox.> > I added popc as solvent around alamethicin after aligning alamethicin in a> > box and centering it in the box and followed same procedure for popc also. Do> > you have any better way?> >> > In theory, that should work just fine, but I don't understand what you mean by> "followed the same procedure for popc." What did you do there? The first part> should be all you need (alamethicin in the box, solvated with popc).> > Alternatively, you can use make_hole.pl or the inflategro script available> through Peter Tieleman's site:> > http://moose.bio.ucalgary.ca/index.php?page=Translate_lipdis> > -Justin> > >> >> > > Date: Sat, 10 Nov 2007 10:22:45 -0500> From: jalemkul at vt.edu> To:> > gmx-users at gromacs.org> Subject: RE: [gmx-users] mdrun error> > Since> > alamethicin works on its own, it suggests to me that the introduction of>> > alamethicin into POPC is what's causing the problem, and judging by the>> > enormous potential energies and forces, it appears to be bad contacts/atomic>> > overlap (at least, that's been the cause of problems in my experience). How>> > are you generating your starting structure?> > -Justin> > >> > Thanks for> > your help. I figured the problem out but am getting an error> > again. I have> > alamethicin in popc and water. Since alamethicin has some non> > standard> > residue i made topology file in text editor and ran mdrun with only> >> > alamethicin. It went fine. But when i am tring to minimize alamethicin in> >> > popc mdrum probably does not recognize the starting of second chain and> > gives> > me following error:> >> > Warning: 1-4 interaction between 164 and> > 169 at distance 3.430 which is> > larger than the 1-4 table size 1.000 nm> >> > These are ignored for the rest of the simulation> > This usually means your> > system is exploding,> > if not, you should increase table-extension in your> > mdp file> > Step= 1, Dmax= 1.0e-02 nm, Epot= 3.25524e+09 Fmax= 1.00321e+09,> > atom=> > 2441> > Step= 2, Dmax= 1.2e-02 nm, Epot= 2.21743e+09 Fmax=> > 1.82388e+08, atom=> > 12852> > Step= 3, Dmax= 1.4e-02 nm, Epot= 1.95672e+09> > Fmax= 7.44135e+07, atom= 262> > Step= 4, Dmax= 1.7e-02 nm, Epot= 1.88109e+09> > Fmax= 4.32188e+07, atom= 260> > Step= 5, Dmax= 2.1e-02 nm, Epot= 1.84989e+09> > Fmax= 2.77292e+07, atom= 262> > Step= 6, Dmax= 2.5e-02 nm, Epot= 1.83083e+09> > Fmax= 1.89783e+07, atom= 258> > Step= 7, Dmax= 3.0e-02 nm, Epot= 1.81606e+09> > Fmax= 9.97167e+06, atom= 253> > Step= 8, Dmax= 3.6e-02 nm, Epot= 1.79660e+09> > Fmax= 2.09557e+07, atom= 258> > Step= 9, Dmax= 4.3e-02 nm, Epot= 1.78793e+09> > Fmax= 1.63547e+07, atom= 259> > Step= 10, Dmax= 5.2e-02 nm, Epot= 1.77532e+09> > Fmax= 7.54157e+06, atom=> > 12539> > Step= 11, Dmax= 6.2e-02 nm, Epot=> > 1.74488e+09 Fmax= 7.42417e+06, atom=> > 12539> > Step= 12, Dmax= 7.4e-02 nm,> > Epot= 1.70998e+09 Fmax= 7.28331e+06, atom=> > 12539> > Step= 13, Dmax=> > 8.9e-02 nm, Epot= 1.66920e+09 Fmax= 7.11508e+06, atom=> > 12539> > Wrote pdb> > files with previous and current coordinates> >> > Back Off! I just backed up> > step13.pdb to ./#step13.pdb.1#> >> > Back Off! I just backed up step14.pdb to> > ./#step14.pdb.1#> > Wrote pdb files with previous and current coordinates> >>> > > my pdb file at 164 to 169 is:> > ATOM 164 CZ PHL 21 44.000 52.840 35.170> > 1.00 0.00> > ATOM 165 HZ PHL 21 44.990 53.260 35.090 1.00 0.00> > ATOM 166 CX> > PHL 21 38.140 50.450 37.160 1.00 0.00> > ATOM 167 OY PHL 21 37.940 49.350> > 38.060 1.00 0.00> > ATOM 168 HY PHL 21 37.040 48.940 37.950 1.00 0.00> > ATOM> > 169 CA ACE 22 53.840 44.410 66.930 1.00 0.00> >> > I think it is not> > recognising different chain. Am i right? Please help me.> >> > _________________________________________________________________> > Check> > out some new online services at Windows Live Ideas—so new they haven’t> >> > even been officially released yet.> >>> >> http://www.msnspecials.in/windowslive/_______________________________________________>> > > gmx-users mailing list gmx-users at gromacs.org> >> > http://www.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> > gmx-users-request at gromacs.org.> > Can't post? Read> > http://www.gromacs.org/mailing_lists/users.php> >> > > >> > =========================================================> > Justin A.> > Lemkul> Graduate Research Assistant> 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> > gmx-users at gromacs.org> http://www.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 gmx-users-request at gromacs.org.> Can't post? Read> > http://www.gromacs.org/mailing_lists/users.php> > _________________________________________________________________> > Call friends with PC-to-PC calling -- FREE> > http://get.live.com/messenger/overview> > > > =========================================================> > Justin A. Lemkul> Graduate Research Assistant> 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 gmx-users at gromacs.org> http://www.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 gmx-users-request at gromacs.org.> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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