[gmx-users] problem with Lipid.itp and dppc.itp
Derrick Guang Yuh Lee
k24dgyl at mun.ca
Wed Oct 29 04:25:02 CET 2003
go here: http://www.gromacs.org/topologies/force_fields.php and grab file:
i had the same problem w/ the dppc128.pdb file from the tieleman's
website, the new force fields should compensate and include the ffgmx.itp
in your top file. that's the process i used so there shouldn't be any
problems, i believe. if anyone see's something wrong, please correct
me. hope it helps.
faculty of Science
Memorial University of Newfoundland
k24dgyl at mun.ca or derrickglee at hotmail.com
"a teacher is never a giver of truth - he is a guide, a pointer to the
truth that each student must find for himself. a good teacher is merely a
- bruce lee
On Tue, 28 Oct 2003, Yuhua Song wrote:
> I download the DPPC64.pdb, dppc.itp and lipid.itp from Peter Tieleman's group website, when I generate the *.tpr file use grompp,
> it shows the following fatal error information:
> Fatal error: Atomtype 'C' not found!
> I do not know what is wrong here. The following is my *.top file
> ; Include forcefield parameters
> #include "lipid.itp"
> ; Include chain topologies
> #include "dppc.itp"
> ; Include water topology
> #ifdef FLEX_SPC
> #include "flexspc.itp"
> #include "spc.itp"
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> [ system ]
> ; Name
> Pure DPPC bilayer with 64 lipids and 3846 water molecules
> [ molecules ]
> ; Compound #mols
> DPPC 64
> SOL 3846
> If you can give me some hints about why this fatal error happened, what
> cause this, I will very appreciate.
> Thank you very much,
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