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
<[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
