[gmx-users] LINCS warning in Position Restraint

Tsjerk Wassenaar tsjerkw at gmail.com
Sun Feb 26 22:57:26 CET 2006

Hi Om Prakash,

The warnings below are serious indicators of trouble and should never be
ignored. It says that you're using the wrong .top file and .gro file
together. Apparently, in one you have the cl- ions and in the other you
haven't. As a consequence of the resulting shift the whole connectivity of
your system is completely messed up, which gives a neat effect: a complete
blow-up in the first step.

Make sure you're .top file and .gro file match. Maybe you put the cl- in the
.top before the sol, whereas they're at the end in the .gro file?

Btw, you may want to use a bit lower -posrefc (I always use 200) for the
position restraint run, to allow your solute to move a bit during the
relaxation. It will move back to the reference position but will allow
better relaxation of the surroundings/hydrogens. And also note that pdb2gmx
doesn't read CONECT statements. It infers sulfur bridges from the
interatomic distances between Cys-SG atoms :)

Hope it helps,


> There was 1 warning during grompp run though.
> --------------------------------------------------------
> Warning: atom names in
> /vol1/people/student1/om/lyso/1OMB_np_gromacs_4/test/pdb.
> top and /vol1/people/student1/om/lyso/1OMB_np_gromacs_4/test/pdb_b4pr.gro
> don't match (CL - HW2)
> .........
> WARNING 1 [file
> "/vol1/people/student1/om/lyso/1OMB_np_gromacs_4/test/pdb.top",
> line 2147]:
>   4933 non-matching atom names
>   atom names from
>   /vol1/people/student1/om/lyso/1OMB_np_gromacs_4/test/pdb.top will be
> used
>   atom names from
>   /vol1/people/student1/om/lyso/1OMB_np_gromacs_4/test/pdb_b4pr.gro will
> be
>   ignored


Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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