[gmx-users] mdrun error

Sun Nov 11 05:20:11 CET 2007

Quoting pragya chohan <pragyachohan at hotmail.com>:

> 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: jalemkul at vt.edu> To:
> gmx-users at gromacs.org> Subject: RE: [gmx-users] mdrun error> > 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/> >
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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/

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