[gmx-users] grompp error in peptide-membrane simulations

[maite lopez]

Thanks Tsjerk

In the begining i tried to create the dppc.gro  executing pdb2gmx (
pdb2gmx_331 -f dppc.pdb -dppc.gro -p dppc.top -i dppc.itp -ffG53a5
-water spc -ignh) i 've gived a lot of warnings.

Warning: Long Bond (34-36 = 4.17214 nm)
Warning: Long Bond (36-37 = 4.13444 nm)
Warning: Long Bond (37-38 = 4.15861 nm)
Warning: Long Bond (38-39 = 4.14343 nm)
Warning: Long Bond (39-40 = 4.14823 nm)
Warning: Long Bond (40-41 = 4.16422 nm)

and in the mailing list said me:
pdb2gmx tries to tie your lipids together. Don't run the membrane
through pdb2gmx.

i've changed the atoms of the dppc.itp  file by the atoms of the DPPC
molecule that appear in the ffG53a5.rtp file (for example LC3 by CH3)
and run grompp , but it gives :
Fatal error:
Atomtype 'C1' not found!

I don´t  know  how  to convert my  lipids to ffG53a5. Could you
explain me briefly?

cheers

Maite



On 3/2/07, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
Hi Maite,
>
> grompp-error... helpful subject :)
> You're trying to combine ffG53a5 and ffgmx. Very bad idea (and not
> readily possible anyway, since atom type definitions and other things
> are incompatible). You have to convert your lipids to ffG53a5. Don't
> try to do it the other way around and convert everything to ffgmx.
> That force field is deprecated.
>
> Best,
>
> Tsjerk
>
> On 3/2/07, maite lopez <lopezmai at gmail.com> wrote:
> > Hi:
> >
> > This is the other part of my last email.
> >
> > I've done many things as suggested in mailing list for example:
> >
> > 1)If i don't include the lipid.itp file      >>>> atomtype LC3 not found
> > or if i put ";" in the line 9 of lipid.itp >>>> atomtype LC3 not found
> > or if i put ";" in the line 9 of lipid.itp and put
> > [ defaults ]
> > ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
> >   1             1               no              1.0     1.0
> >
> > in the .top file, the same error comes.
> >
> > 2)I've been using the ffgmx.itp and i've removed the lipid.itp of the
> > .top file, but it gives a fatal error  :
> > Atomtype 'HC' not found!  (this is a atom of the peptide)
> >
> > I created the peptide.gro with this force field and i did the last
> > steps again but a Fatal error:
> > Atomtype 'C1' not found!  (in the DPPC membrane)
> >
> > 3)I've included the ffgmxnb.itp and ffgmxbon.itp files in the
> > ffG53a5.itp, and the atomtype in the ffG53a5.atp, but of course it
> > overwrites the atoms.
> >
> > 4)I've include the lipid.itp in the ffG53a5nb.itp , i've added the
> > atomtype in the ffG53a5.atp  and i've put ";" in the line
> > 9 of lipid.itp: the error is atomtype CA not found or the LP2 not
> > found. I cut and paste the corresponding entries from the lipid.itp
> > file into the
> >  correct non-bonding file, but this doesn't result.
> >
> > 5)i've changed the atoms of the dppc.itp file by the atoms of the DPPC
> > molecule that appear in the ffG53a5.rtp file (for
> > example LC3 by CH3) and it gives :
> > Fatal error:
> > Atomtype 'C1' not found!
> >
> >
> >
> > Any help will be highly appreciated.
> >
> > Maite
> > _______________________________________________
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
> F: +31-30-2537623
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