Anna Marabotti wrote:
Dear Justin,
AAARRRGGGHH! The last case indicated in the wiki section about 0 topology was
MY case: probably I was using a
.mdp file that was created with Windows. When I re-wrote my em.mdp file using
vi, it worked!!
I'm sorry for all this waste of time, but as I told some days ago, I've
problems in seeing the contents of the
GROMACS site (old and new), and I could access to this information only through
the link you sent me...
A little suggestion for developers: would it be possible to insert an error
message more indicative for this
problem? I don't pretend that computers do everything I need, but it would be
nice that they could at least
suggest me a solution in a less cryptic way when I have such a trivial problem,
so I can avoid boring the
developers themselves...;-)
It's actually an extremely rare cause for the problem, and adding text
about DOS line endings there would confuse people, I think. Future
releases of GROMACS are supposed to have links to the Errors wiki page,
and this kind of information belongs there.
Preventing this problem is simple - even when working on a Windows
machine, don't use its tools for editing files! Use Cygwin, or tunnel
emacs out over X, or use emacs -nw, or vi. In extremis run everything
through dos2unix.
You were unlucky to have been compounding the problem with other
mistakes, though :-)
Mark
Thank you to all for collaboration and best regards
Anna
Anna Marabotti wrote:
Dear all,
as requested, I'm copying here the SDS.itp file (it should be not too big):
; This file was generated by PRODRG version AA081006.0504
; PRODRG written/copyrighted by Daan van Aalten
; and Alexander Schuettelkopf
;
; Questions/comments to [email protected]
;
; When using this software in a publication, cite:
; A. W. Schuettelkopf and D. M. F. van Aalten (2004).
; PRODRG - a tool for high-throughput crystallography
; of protein-ligand complexes.
; Acta Crystallogr. D60, 1355--1363.
[ moleculetype ]
; Name nrexcl
SDS 3
OK, as I thought, if you #include "SDS.itp" you should NOT specify a separate
[moleculetype] directive in your system .top file.
<snip>
As I told sometimes ago, I obtained this file from PRODRG starting from a
SDS.pdb file that I created using
SDS coordinates found in another .pdb file (I simply copied and pasted the SDS
coordinates in a new file and
called it SDS.pdb). For my simulations, however, I used the SDS.gro file and
SDS.itp file generated by
PRODRG.
I notice that the section [ moleculetype] is present in SDS.itp, but nothing
changes if I erase the [
moleculetype ] section for SDS in my_prot.top: in all cases it doesn't work...
I also copied and pasted the entire topology of SDS explicitly into my_prot.top
instead of typing #include
"SDS.itp", and nothing changed again...
Well, the .itp file itself seems to have been properly generated.
Concerning the order of molecules in the last [ molecules ] section, I changed
it several times, and nothing
changed...
I'm still with an unclarified question: why genbox did not create by itself all
corrections necessary to the
original .top file when I used the -ci -nmol options? I added the -p flag but
it doesn't change the topology
by itself (as it should do, in my opinion).
It would be nice if the computers did everything for us, wouldn't it? :) Maybe
one day. It looks like automated updates only work for addition of water.
Perhaps this can be a future improvement to genbox.
Have you read the error page for your problem:
http://oldwiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
There is a specific section on the case where grompp detects 0 coordinates in
the .top that might be relevant.
-Justin
Thank you again
Anna
______________________________________________
Anna Marabotti, Ph.D.
Laboratory of Bioinformatics and Computational Biology
Institute of Food Science, CNR
Via Roma 64
83100 Avellino (Italy)
Phone: +39 0825 299651
Fax: +39 0825 781585
Skype: annam1972
E-mail: [email protected]
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
____________________________________________________
"If you think you are too small to make a difference, try sleeping with a
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