[gmx-users] Problems using grompp and amber force field

[root]

Dear GROMACS user:
David and Mark, thanks by our comments, suggestions and questions. If
our response is confused, please require us copies of output files (or
fragment). 

The procedure to simulate the DNA dodecamer was:

1) We generate the DNA topology and coordinates in gromacs format (with
the amber03 force field ) using the pdb2gmx program:

pdb2gmx -f dickerson.pdb -o dick.gro -p dick.top -water spce

2) and we obtain the box with the dodecamer plus water coordinates
using editconf and genbox:

editconf -f dick.gro -o dick03.pdb -bf triclinic -box 6 5 6 -angle 90 90
90
genbox -cp dick03.pdb -cs -o dick02.pdb -p dick.top

3) with the files dick03.pdb and dick.top we run grompp:

grompp -f em -c dick02.pdb -p dick.top -o dick.tpr -pp topo2.top
                         
The output of the program indicate
...
creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
checking input for internal consistency...
calling /usr/bin/cpp...
In the file included of /usr/local/gromacs/share/top/ffamber03.itp:19,
                 de dick.top:11:
/usr/local/gromacs/share/top/ffamber03bon.itp:538:22: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:541:22: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:543:22: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:547:21: 
warning: spaces are absent in target after the name of macro
/usr/local/gromacs/share/top/ffamber03bon.itp:559:19: 
warning: spaces are absent in target after the name of macro
processing topology...
Generated 2701 of the 2701 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2701 of the 2701 1-4 parameter combinations
-------------------------------------------------------
Program grompp, VERSION 3.3.1
Source code file: toppush.c, line: 758

Fatal error:
Atoms in the .top are not numbered consecutively from 1

-------------------------------------------------------

We tested the dick.top file, and we verified that the atoms are numbered
consecutively from 1 to 758. 
We analyzed the warning messages. They correspond to a format of
desciption of a dihedral angle. For example the 538:22 warning
correspond to le line 538 column 22

#define proper_X_CT_N*_X  
and there are a format problem with the * simbol.

we don't know that to do still with this.


Other coments: Previosly,  we consult the gromacs mailing list,
searching similar DNA simulation and finding suggest about the opls-na
and amber force field. Initially, we attempted to obtain a topology with
the opls-na force fied, but fequent error mesagges about the format of
the input file were generated. In consecuence, we thinked that there was
differences in the input format to the differente versions of the
gromacs package. Of course, it is only a hypothesis.

Thanks in advance
 
Mario Campo and Griselda Corral
Fac. de Cs. Exactas y Naturales
UNLPam