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

maite lopez lopezmai at gmail.com
Fri Mar 2 22:17:24 CET 2007


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.


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