Hi,
You need to make sure you have an #ifdef _FF_AMBER statement in the spc.itp
file for it to work correctly, as Mark has suggested. This has been
discussed on the list before.
Tom
--On Friday, December 07, 2007 17:57:47 +0000 Shozeb Haider
<[EMAIL PROTECTED]> wrote:
Hi,
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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----------------------
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.
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