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 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 d...@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 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: amarabo...@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" _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php