[gmx-users] testing ligand-protein system in Release Candidate 3 of version 3.3

David spoel at xray.bmc.uu.se
Mon Oct 10 20:00:53 CEST 2005

On Mon, 2005-10-10 at 12:58 +0200, mollica.luca at hsr.it wrote:
> dear users,
> we are trying to set up a novel installation of GROMACS on an IBM 
> eServer BladeCenter (56 procs, 28 nodes, myrinet) using the GMX 3.3 - 
> rc3.
> The first tests seem to be really ok, but only in case of systems with 
> protein, water and ions. I have tested the set up also with a protein-
> ligand system, but I have encountered a strange problem that has never 
> occourred in 3.2.1 stable version. 
> Running grompp on EXACTLY THE SAME sytem and files theat used to give 
> successful reults and work fine on 3.2.1 version on the same machine
> (a version that has been left to be alive on the first half of nodes), 
> I got this error that seems to be a typical topology error, happening 
> in coincidence with the presence (in the ligand topology file) of 
> dihedral angles (since line 300 until the end of the file):
> Generated 1284 of the 1485 non-bonded parameter combinations
> ERROR 2 [file "ligand.itp", line 300]:
>    Too many parameters

please post relevant section of the file.

There have been some changes in topology file format, but it should be
backwards compatible.

> etc etc ... until reaching the linmit of 10 errors and stopping the 
> grompping process invoking an error in source code fatal.c in line 416.
> What's going on with my ligand ? Everything works pretty well with 
> 3.2.1 installation, but it is not working with this version 3.3.rc3.
> Is a release related problem ? Or does it depend on some changes that 
> I have to make in the set up of th files for running MD simulation ?
> thanx a lot
> LM
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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
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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