[gmx-users] DNA adduct simulation: grompp error

[Nathalie Geneste]

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:
n.geneste at ism.u-bordeaux1.fr
******************