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<body class='hmmessage'>Thanks Justin for your reply. I am generating the starting structure through genbox.<BR>
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?<BR><BR><BR><BR><BR>
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> Date: Sat, 10 Nov 2007 10:22:45 -0500<BR>> From: jalemkul@vt.edu<BR>> To: gmx-users@gromacs.org<BR>> Subject: RE: [gmx-users] mdrun error<BR>> <BR>> Since alamethicin works on its own, it suggests to me that the introduction of<BR>> alamethicin into POPC is what's causing the problem, and judging by the<BR>> enormous potential energies and forces, it appears to be bad contacts/atomic<BR>> overlap (at least, that's been the cause of problems in my experience). How<BR>> are you generating your starting structure?<BR>> <BR>> -Justin<BR>> <BR>> ><BR>> > Thanks for your help. I figured the problem out but am getting an error<BR>> > again. I have alamethicin in popc and water. Since alamethicin has some non<BR>> > standard residue i made topology file in text editor and ran mdrun with only<BR>> > alamethicin. It went fine. But when i am tring to minimize alamethicin in<BR>> > popc mdrum probably does not recognize the starting of second chain and gives<BR>> > me following error:<BR>> ><BR>> > Warning: 1-4 interaction between 164 and 169 at distance 3.430 which is<BR>> > larger than the 1-4 table size 1.000 nm<BR>> > These are ignored for the rest of the simulation<BR>> > This usually means your system is exploding,<BR>> > if not, you should increase table-extension in your mdp file<BR>> > Step= 1, Dmax= 1.0e-02 nm, Epot= 3.25524e+09 Fmax= 1.00321e+09, atom=<BR>> > 2441<BR>> > Step= 2, Dmax= 1.2e-02 nm, Epot= 2.21743e+09 Fmax= 1.82388e+08, atom=<BR>> > 12852<BR>> > Step= 3, Dmax= 1.4e-02 nm, Epot= 1.95672e+09 Fmax= 7.44135e+07, atom= 262<BR>> > Step= 4, Dmax= 1.7e-02 nm, Epot= 1.88109e+09 Fmax= 4.32188e+07, atom= 260<BR>> > Step= 5, Dmax= 2.1e-02 nm, Epot= 1.84989e+09 Fmax= 2.77292e+07, atom= 262<BR>> > Step= 6, Dmax= 2.5e-02 nm, Epot= 1.83083e+09 Fmax= 1.89783e+07, atom= 258<BR>> > Step= 7, Dmax= 3.0e-02 nm, Epot= 1.81606e+09 Fmax= 9.97167e+06, atom= 253<BR>> > Step= 8, Dmax= 3.6e-02 nm, Epot= 1.79660e+09 Fmax= 2.09557e+07, atom= 258<BR>> > Step= 9, Dmax= 4.3e-02 nm, Epot= 1.78793e+09 Fmax= 1.63547e+07, atom= 259<BR>> > Step= 10, Dmax= 5.2e-02 nm, Epot= 1.77532e+09 Fmax= 7.54157e+06, atom=<BR>> > 12539<BR>> > Step= 11, Dmax= 6.2e-02 nm, Epot= 1.74488e+09 Fmax= 7.42417e+06, atom=<BR>> > 12539<BR>> > Step= 12, Dmax= 7.4e-02 nm, Epot= 1.70998e+09 Fmax= 7.28331e+06, atom=<BR>> > 12539<BR>> > Step= 13, Dmax= 8.9e-02 nm, Epot= 1.66920e+09 Fmax= 7.11508e+06, atom=<BR>> > 12539<BR>> > Wrote pdb files with previous and current coordinates<BR>> ><BR>> > Back Off! I just backed up step13.pdb to ./#step13.pdb.1#<BR>> ><BR>> > Back Off! I just backed up step14.pdb to ./#step14.pdb.1#<BR>> > Wrote pdb files with previous and current coordinates<BR>> ><BR>> > my pdb file at 164 to 169 is:<BR>> > ATOM 164 CZ PHL 21 44.000 52.840 35.170 1.00 0.00<BR>> > ATOM 165 HZ PHL 21 44.990 53.260 35.090 1.00 0.00<BR>> > ATOM 166 CX PHL 21 38.140 50.450 37.160 1.00 0.00<BR>> > ATOM 167 OY PHL 21 37.940 49.350 38.060 1.00 0.00<BR>> > ATOM 168 HY PHL 21 37.040 48.940 37.950 1.00 0.00<BR>> > ATOM 169 CA ACE 22 53.840 44.410 66.930 1.00 0.00<BR>> ><BR>> > I think it is not recognising different chain. Am i right? Please help me.<BR>> > _________________________________________________________________<BR>> > Check out some new online services at Windows Live Ideas—so new they haven’t<BR>> > even been officially released yet.<BR>> ><BR>> http://www.msnspecials.in/windowslive/_______________________________________________<BR>> > gmx-users mailing list gmx-users@gromacs.org<BR>> > http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> > Please search the archive at http://www.gromacs.org/search before posting!<BR>> > Please don't post (un)subscribe requests to the list. Use the<BR>> > www interface or send it to gmx-users-request@gromacs.org.<BR>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR>> ><BR>> <BR>> <BR>> <BR>> =========================================================<BR>> <BR>> Justin A. Lemkul<BR>> Graduate Research Assistant<BR>> Department of Biochemistry<BR>> Virginia Tech<BR>> Blacksburg, VA<BR>> jalemkul@vt.edu | (540) 231-9080<BR>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/<BR>> <BR>> =========================================================<BR>> _______________________________________________<BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at http://www.gromacs.org/search before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the <BR>> www interface or send it to gmx-users-request@gromacs.org.<BR>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR><BR><br /><hr />Call friends with PC-to-PC calling -- FREE <a href='http://get.live.com/messenger/overview' target='_new'>Try it now!</a></body>
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