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: > [email protected]> 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:> > > [email protected]> 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 [email protected]> >> > > 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> > > [email protected]> 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 > [email protected]> 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/ ========================================================= _______________________________________________ gmx-users mailing list [email protected] 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
