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

[David van der Spoel]

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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