From: faride badalkhani (farideh.khamseh_at_gmail.com)
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 !
GROUP
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
DONOR O1 HA
ACCEPTOR O1
PATCHING FIRS NONE LAST NONE
Any help will be appreciated.
Regards,
Farideh
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