From: Jeff Comer (jeffcomer_at_gmail.com)
Date: Tue Apr 26 2016 - 16:14:50 CDT
What's the mass of the atom 6?
Jeffrey Comer, PhD
Institute of Computational Comparative Medicine
Nanotechnology Innovation Center of Kansas State
Kansas State University
Office: P-213 Mosier Hall
On Mon, Apr 25, 2016 at 10:42 AM, faride badalkhani <
> 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
> DONOR O1 HA
> ACCEPTOR O1
> PATCHING FIRS NONE LAST NONE
> Any help will be appreciated.
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