From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Thu Jul 10 2014 - 17:28:08 CDT
Most probably, the angle was not included in the psf generation. If you
used psfgen , you might need a "auto angles dihedrals" or "regenerate
angles dihedrals" statement or something like that (I use CHARMM so I
don't know the exact syntax for psfgen).
On 07/05/2014 03:05 AM, Fulu Zheng wrote:
> Dear All,
>
> I add a CTER to the LYS residue, but the distance between two O atoms in
> the CTER group becomes unusually small (0.271 angstrom) during the MD
> simulation.
>
> The CTER group used in my simulation is as follows:
>
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> PRES CTER -1.00 ! standard C-terminus
> GROUP ! use in generate statement
> ATOM C CC 0.34 ! OT2(-)
> ATOM OT1 OC -0.67 ! /
> ATOM OT2 OC -0.67 ! -C
> DELETE ATOM O ! \\
> BOND C OT2 ! OT1
> DOUBLE C OT1
> IMPR C CA OT2 OT1
> ACCEPTOR OT1 C
> ACCEPTOR OT2 C
> IC N CA C OT2 0.0000 0.0000 180.0000 0.0000 0.0000
> IC OT2 CA *C OT1 0.0000 0.0000 180.0000 0.0000 0.0000
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
> The parameters for OC in VDW is as follows:
>
> OC 0.000000 -0.120000 1.700000 ! ALLOW POL ION
> ! JG 8/27/89
>
> Any idea about this problem?
>
> Thank you so much!
>
> Fulu
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