[gmx-users] Error message with grompp

[Dallas B. Warren]

Deepa,

> I manually made a topology file for phenol on the basis of the Tyr 
> topology and when I run grommp with this .itp file included I get the 
> following error message which I do not understand.
> ---------------------------------------------------------
> Program grompp, VERSION 3.3
> Source code file: topio.c, line: 405
> 
> Fatal error:
> Found a second defaults directive, file 
> "/usr/local/gromacs/share/gromacs/top/ffG43a2.itp", line 6
> -----------------------------------------------------------
> Can somebody tell me what that means and what i will have to 
> change for the grompp to work?

For future reference, try searching the GROMACS website at
http://www.gromacs.org/search by placing the error message that you
receive.  If you did that you would have found that there is a number of
threads where this error is discussed, including the solution or why it
has occurred ....

http://www.gromacs.org/pipermail/gmx-users/2003-July/006147.html

"You are probably including the forcefield twice (perhaps both from 
lipids.itp and the main xxx.top). Alternatively, lipids.itp might 
contain a full forcefield declaration too."

and .....

http://www.gromacs.org/pipermail/gmx-users/2003-June/005793.html

"chek all itp files. Only one should include ffgmx.itp
if your protein itp comes from pdb2gmx you probably have another one
there."

Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9073
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.