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 ><[EMAIL PROTECTED]> >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 > > <[EMAIL PROTECTED]> > > Responder a: > > Discussion list for GROMACS users > > <gmx-users@gromacs.org> > > Para: > > Discussion list for GROMACS users > > <gmx-users@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@gromacs.org > >> http://www.gromacs.org/mailman/listinfo/gmx-users > >> Please search the archive at > > http://www.gromacs.org/search before posting! > >> Please don't post (un)subscribe requests to the list. Use the > >> www interface or send it to [EMAIL PROTECTED] > >> Can't post? Read > > http://www.gromacs.org/mailing_lists/users.php > > > > > > -- > > 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 > > [EMAIL PROTECTED] [EMAIL PROTECTED] > > http://folding.bmc.uu.se > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > ++++++++++++ > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at > > http://www.gromacs.org/search before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/ > > users.php > > > > > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > _______________________________________________ > 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 > [EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys > > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php