From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri May 29 2009 - 15:00:51 CDT
I have never used autopsf so I can't say for sure what is happening.
Can you look at the first few lines of your psf file and confirm that
for the water segments, you see auto angles dihedrals?
Also, you can check the psf file to check if there are angles present
for any water indices.
On May 29, 2009, at 2:30 PM, enz1+@pitt.edu wrote:
> The modified topology file (using the GUI Autopsf-generator) is the
> same
> one as top_all27_prot_lipid.inp only with the bond between the H atoms
> deleted.
> Other than that its the same, i.e,
>
>
> RESI TIP3 0.000 ! tip3p water model, generate using noangle
> nodihedral
> GROUP
> ATOM OH2 OT -0.834
> ATOM H1 HT 0.417
> ATOM H2 HT 0.417
> BOND OH2 H1 OH2 H2 ! (last bond needed for shake deleted)
> ANGLE H1 OH2 H2 ! required
> ACCEPTOR OH2
> PATCHING FIRS NONE LAST NONE
>
>
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