For the missing whitespace warning you need cpp = /lib/cpp -traditional in
you .mdp file.
For the error you most likely do not have an #ifdef _FF_AMBER statement in
you spc.itp file.
These have both been discussed on the list before so search there for more
details and also the ffamber website:
http://chemistry.csulb.edu/ffamber/
As for your choice of forcefield (and parameterising your adduct) this has
been discussed numerous times before (including recently) so again search
the mailing list or the gromacs wiki.
Tom
--On Wednesday, February 20, 2008 16:09:32 +0100 Nathalie Geneste
<[EMAIL PROTECTED]> wrote:
Dear users,
I have some problems to launch a simulation with my molecular system
including 2 strands DNA + benzo[a]pyrene adduct.
After some trials with default gromacs force fields, I downloaded
ffamber99.
I have 2 problems:
1) my benzo[a]pyrene adduct is not recognized by ffamber99. Could you
propose me a force field compatible with my system ?
2) If I ignore my adduct, we obtained with success my topolgy files but
now I got the following error with grompp:
...
checking input for internal consistency...
calling /usr/bin/cpp...
In file included from /usr/share/gromacs/top/ffamber99.itp:20,
from 1AXV_mod4.top:11:
/usr/share/gromacs/top/ffamber99bon.itp:518:22: warning: missing
whitespace after the macro name
/usr/share/gromacs/top/ffamber99bon.itp:520:22: warning: missing
whitespace after the macro name
/usr/share/gromacs/top/ffamber99bon.itp:521:22: warning: missing
whitespace after the macro name
/usr/share/gromacs/top/ffamber99bon.itp:524:21: warning: missing
whitespace after the macro name
/usr/share/gromacs/top/ffamber99bon.itp:535:19: warning: missing
whitespace after the macro name
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 gromppEkqU9b
-------------------------------------------------------
Program grompp, VERSION 3.3.1
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)
-------------------------------------------------------
Does anybody has an explanation ?
Regards,
Nathalie
--
******************
Dr. N. GENESTE
Groupe LPTC
ISM - UMR 5255 CNRS
Université Bordeaux I
Phone.: 05 40 00 28 43
Fax: 05 40 00 22 67
******************
Nouvelle adresse:
[EMAIL PROTECTED]
******************
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----------------------
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.
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