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

[TJ Piggot]

Hi,

I think if you set "cpp = /lib/cpp -traditional" in your .mdp file then it 
should get rid of the warnings about "spaces are absent in target after the 
name of macro". For more info see 
<http://folding.stanford.edu/ffamber/FAQ.html>

Tom

--On 07 May 2007 20:42 +0200 David van der Spoel <spoel at xray.bmc.uu.se> 
wrote:

> root wrote:
>> 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
>
> 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.
>>
>>
>> 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
>>
>>
>>
>>
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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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----------------------
TJ Piggot
t.piggot at bristol.ac.uk
University of Bristol, UK.