[gmx-users] More ATP errors

Anton Feenstra feenstra at chem.vu.nl
Wed Dec 10 09:13:01 CET 2003

Raj Badhan wrote:

> Dear Sirs,
> After hours of trying to get my simulation to run with ATP as a 
> ligand I have almost given up all hope.
> ATP is the ligand within my protein.
> I can run an em protocol with the protein alone and with the ligand 
> alone, but not with both together, as MDRUN always crashes.
> I have checked for bad contacts and there are none.
> Any suggestions? I am running this on the windows ported version 
> of gromacs, and below is my EM.MDP file.
> Has anyone been able to use ATP as a ligand and got the 
> simulations to work? If so, I would appreciate any 
> ideas/suggestions on how they got their simulation to work.

If both protein and ATP run without errors, the problem *must* be
in the contacts. Can you run at least (a few steps of) EM on the
complex? Then, you can have a look at energy values and see if some
of them are 'way' off. You can compare to those in the protein and
ATP only simulations.

Have you also tried MD of the protein and ATP isolated? For testing
you could even do it in vacuum first, and then try it solvated also.

The only other thing I could think about, is some strange feature
(bug?) of your viewing program, which makes you think the complex is
OK, but it isn't. Have you tried with different programs (e.g., vmd
rasmol, ProteinExplorer)?

Finally, maybe a bit silly, but I've seen it go wrong too often, are
you sure you are always using the right versions of the different files?
It may help to start over in a new directory, putting in single files
one at a time and checking each of them very carefully so you can be
sure that of each file (e.g. .top, .gro, .pdb, .mdp) there is only
one version and no errors...

Wish you good luck!


  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
|             | "If You See Me Getting High, Knock Me Down"           |
|             | (Red Hot Chili Peppers)                               |

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