Constraint failure in RATTLE algorithm for atom 6!

From: faride badalkhani (
Date: Mon Apr 25 2016 - 10:42:52 CDT

Dear NAMD users,

I am trying to simulate a hyperbranched polymer in a water box. I defined
the patches and built the Protein Structure File (PSF) using a tcl command,
and there was nothing strange in psf file format. when I run a NVT
simulation for 500 ps I got this error message:

ERROR: Constraint failure in RATTLE algorithm for atom 6!
ERROR: Constraint failure; simulation has become unstable.
ERROR: Exiting prematurely; see error messages above.

So, I reviewed NAMD mailing list and checked periodic cell size. I had
minimized the system for 25 ps. I tried looking at my psf and pdb files in
VMD. There was no atom with (0, 0, 0) coordinates.
I set the MARGIN parameter to 5 in the NAMD configuration file.

But I got the same error. Therefore, I tried the simulated annealing in
vacuum. But, it does not work, too.

Atom 6 (in fact, 5) is an internal alkyne carbon! and the residue has a
shape of

RESI POC -0.235 !
ATOM HA H 0.421
ATOM O1 OH1 -0.899 !
ATOM C1 CT2 0.198 ! H1
ATOM H1 HA2 0.090 ! __ |
ATOM H2 HA2 0.090 ! H3--C3==C2--C1--O1--HA
ATOM C2 CGT1 -0.015 ! |
ATOM C3 CGT2 -0.410 ! H2
ATOM H3 HGP 0.290 !
BOND H3 C3 C3 C2 C2 C1 C1 O1
BOND C1 H1 C1 H2 O1 HA

Any help will be appreciated.


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