[gmx-users] POPC simulation

Steffen Wolf swolf at bph.rub.de
Wed May 24 10:12:34 CEST 2006

Arindam Ganguly wrote:
> 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
Hm, strange, but OK, another idea: I just saw that your setup 
essentially trippels the callups for the necessary forcefield 
parameters: You can not only transfer the atomtypes to ffgmxbon.itp, but 
the rest of the included parameters into ffgmxbon.itp and ffgmxnb.itp as 
well, so you won't have to call lipid.itp. Next thing: why are you 
including ffgmx2nb.itp and ffgmx2bon.itp explicitly? They are already 
set up by calling ffgmx.itp in the beginning, you're just overriding 
everything again. So: after modifying lipid.itp, you should do fine with
#include "ffgmx.itp"
#include "popc.itp"
Dipl.-Chem. Steffen Wolf
Department of Biophysics
University of Bochum
ND 04/67
44780 Bochum
Tel: +49 (0)234 32 28363
Fax: +49 (0)234 32 14626
E-Mail: swolf at bph.rub.de
Web: http://www.bph.rub.de 

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