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

[Erik Marklund]

As someone already mentioned, the following can be found among the  
AMBERport FAQ:

 >>
Why do I get a grompp warning "missing white space after `#define  
proper_*'?"
Set "cpp = /lib/cpp -traditional" in your .mdp file to remove these  
warnings, which result from the use of the N* atom type of the AMBER  
family of force fields and can be ignored.
<<

Did you try doing that?

Good luck!

/Erik

7 maj 2007 kl. 22.29 skrev 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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_______________________________________________
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,	75124 Uppsala, Sweden
phone:	+46 18 471 4537		fax: +46 18 511 755
erikm at xray.bmc.uu.se	http://xray.bmc.uu.se/molbiophys