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

Anna Marabotti anna.marabotti at isa.cnr.it
Thu Jun 18 17:42:09 CEST 2009

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...;-)

Thank you to all for collaboration and best regards

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.


> 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:


There is a specific section on the case where grompp detects 0 coordinates in 
the .top that might be relevant.


> 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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