[gmx-users] AMBER ff99SB port problems

Shozeb Haider shozeb.haider at pharmacy.ac.uk
Fri Dec 7 18:57:47 CET 2007


I was wondering if any has expertise in using Amber ff99SB port (Pande's 
lab). I am currently using port for 3.3.1 version of gromacs.

When I solvate my protein and run grompp to generate a tpr file, it 
gives me the following error

checking input for internal consistency...
calling /lib/cpp -traditional...
processing topology...
Generated 2628 of the 2628 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2628 of the 2628 1-4 parameter combinations
Cleaning up temporary file gromppXORFn5
Program grompp, VERSION 3.3
Source code file: toppush.c, line: 1108

Fatal error:
[ file "/usr/share/gromacs/top/spc.itp", line 41 ]:
             Atom index (1) in settles out of bounds (1-0)

 From what it seems that the program is unable to communicate with 
spc.itp file. However that should not be the case since the program 
routinely does that when I run using other gromacs force fields. I have 
also explicitly included the /share/gromacs/top direcly as well

I have the following lines in my preprocessor :
cpp                 =  /lib/cpp -traditional  ; prepocessor of the 
current machine
include             =  -I/usr/share/gromacs/top
define              =

Any suggestions would be much appreciated.

Many thanks

Shozeb Haider
The London School of Pharmacy

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