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

[Tsjerk Wassenaar]

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