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?
> 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
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> =========================================================> > 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/> >
> =========================================================>
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