[gmx-users] POPC simulation

[Arindam Ganguly]

Hi Steffen,
Thanks very much for the prompt reply. i made the changes as mentioned such
that my popc.top looks like this :-
#include "ffgmx.itp"
#include "lipid.itp"
#include "popc.itp"
#include "ffgmx2nb.itp"
#include "ffgmx2bon.itp"

however is still get the same message "Fatal error: Bonded/nonbonded atom
type 'LP2' not found!".
i forgot to mention one thing in my earlier mail that the ffgmx.atp file
provided with originally from GROMACS , i replaced the contents of it by the
contents present in the ffgmx.atp file present in the ffgmx_lipids folder as
downloaded from the Gromacs website.


my understanding is this shouldn;t cause the problem since the orinigal
ffgmx.atp file ( as provided by gromacs) doesn;t contain all the atom types.
in fact when i compared the both files i found that the ffgmx.atp file (from
ffgmx_lipids folder ) has the following extra entries which were required
for the lipid simulation. i am kind of confused as to where i am committig
the mistake. plz help. thanks.

Arindam Ganguly







Hi Arindam,
you've simply got to switch two lines in the *.top file: lipid.itp has
to be called by the topology before popc.itp, as it contains the
information on atomtypes for GROMACS. So:

#include "lipid.itp"
#include "popc.itp"

should work just fine.
Greetings
Steffen
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