Shozeb Haider 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
Nope, it's finding spc.itp just fine. Have a look at what's in there,
and if necessary check out http://wiki.gromacs.org/index.php/cpp for
some hints on how it's working. Each GROMACS forcefield #defines a
variable, and since this AMBER port is non-standard, the standard SPC
file doesn't deal with that possibility. So when parsing spc.itp, grompp
doesn't see any atom definitions. The first thing it does see is the
settles, which are out of bounds because there are zero atoms. To fix
this, either use some ffamber_spc.itp if one exists, or make one.
Mark
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