[gmx-users] Problems using grompp and amber force field
root
mario at exactas.unlpam.edu.ar
Tue May 8 02:27:03 CEST 2007
Dear GROMACS user:
Erik and Tom thanks by the comments, too. Sorry, I read the FAQ pages of
http://folding.stanford.edu and now I understand your comments.
We tried with cpp = /lib/cpp -traditional in the mdp file. The warning
desapears, but the error messages is similar.
(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 download the ffamber_v3.3.1-doc.tar.gz, that we considered that
correspond to the 3.3.1 version of GROMACS.
Is this correct?
Thanks in advance.
Mario
El lun, 07-05-2007 a las 23:17 +0200, Erik Marklund escribió:
> 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:
>
> 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:
> > 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
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> gmx-users mailing list gmx-users at gromacs.org
> >> http://www.gromacs.org/mailman/listinfo/gmx-users
> >> Please search the archive at
> > http://www.gromacs.org/search before posting!
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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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> >
> >
> >
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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
>
>
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