[gmx-users] Re: Re: protein in SDS/water

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jun 18 19:18:06 CEST 2009

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 :-)


> 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 dava at davapc1.bioch.dundee.ac.uk
>> ;       
>> ;       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
>> 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: amarabotti at isa.cnr.it
>> 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 mosquito"
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