Pragya, I just realized that I may have read your message incorrectly. If you'd like to send me your PDB file off-list, I'd be happy to have a look.
-Justin Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>: > Quoting pragya chohan <[EMAIL PROTECTED]>: > > > 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 > > Looks like the listserv ate the PDB file, but from your description it sounds > like you've generated some severe atomic overlap. Simply pasting coordinates > of a protein into a membrane is sure to cause bad contacts. The proper > procedure would be to create a cavity within the membrane and place the > protein > in it (i.e., make_hole.pl, inflategro, as I previously suggested), or using > genbox, which you originally said you did. Try this (assuming you have the > box > dimensions correct): > > $ genbox -cp alamethicin.gro -cs popc.gro -o system.gro > > -Justin > > > > > Pragya > > > > > > > > > Date: Sat, 10 Nov 2007 12:42:01 -0500> From: [EMAIL PROTECTED]> To: > > gmx-users@gromacs.org> Subject: RE: [gmx-users] mdrun error> > Quoting > pragya > > chohan <[EMAIL PROTECTED]>:> > > 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: [EMAIL PROTECTED]> To:> > > >> > > > > > gmx-users@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 Ideasso new they > > havent> >> > even been officially released yet.> >>> >> > > > http://www.msnspecials.in/windowslive/_______________________________________________>> > > > > gmx-users mailing list gmx-users@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> > [EMAIL PROTECTED]> > 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> [EMAIL PROTECTED] | (540) 231-9080>> > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/> >> > > > =========================================================>> > > > _______________________________________________> gmx-users mailing list> > > > gmx-users@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 [EMAIL PROTECTED]> 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> [EMAIL PROTECTED] | (540) 231-9080> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/> > > > =========================================================> > > _______________________________________________> gmx-users mailing list > > gmx-users@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 [EMAIL PROTECTED]> Can't post? Read > > http://www.gromacs.org/mailing_lists/users.php > > _________________________________________________________________ > > Windows Live Spaces is here! Its easy to create your own personal Web > site. > > http://spaces.live.com/?mkt=en-in > > > > ========================================================= > > Justin A. Lemkul > Graduate Research Assistant > Department of Biochemistry > Virginia Tech > Blacksburg, VA > [EMAIL PROTECTED] | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ > > ========================================================= ========================================================= Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ========================================================= _______________________________________________ gmx-users mailing list gmx-users@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 [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php