[gmx-users] mdrun error

[Justin A. Lemkul]

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.> >
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> =========================================================> > 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/> >
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=========================================================

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/

=========================================================