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

[root]

David and GROMACS users:
Sorry we changed the error message in ...

/usr/local/gromacs/share/top/ffamber03bon.itp:541:22:  warning: spaces
are absent in target after the name of macro
        
because of the original message was in spanish.

We checked these files above. We run GROMACS in fedora 6.0
We analyzed the warning messages. They correspond to a format of
description 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 * symbol.
 
 we don't know that to do still with this.
 

Thanks in advance

root wrote:
                                De: 
David van der Spoel
<spoel at xray.bmc.uu.se>
                       Responder a: 
Discussion list for GROMACS users
<gmx-users at gromacs.org>
                              Para: 
Discussion list for GROMACS users
<gmx-users at gromacs.org>
                            Asunto: 
Re: [gmx-users] Problems using
grompp and amber force field
                             Fecha: 
Mon, 07 May 2007 20:42:51 +0200
(15:42 ART)
        
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...
        
        check the files above. is the error message correct? then fix
        it.
        
        what kind of system are you running this on?

> 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.
        > 
        > 
        > 
        > Thanks in advance
        >  
        > Mario Campo and Griselda Corral
        > Fac. de Cs. Exactas y Naturales
        > UNLPam 
        > 
        > 
        > 
        > 
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        -- 
        David.
        ________________________________________________________________________
        David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics
        group,
        Dept. of Cell and Molecular Biology, Uppsala University.
        Husargatan 3, Box 596,          75124 Uppsala, Sweden
        phone:  46 18 471 4205          fax: 46 18 511 755
        spoel at xray.bmc.uu.se    spoel at gromacs.org
        http://folding.bmc.uu.se
        ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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