From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Wed Jun 26 2013 - 14:07:09 CDT
Hi James,
On 06/26/2013 01:56 AM, James Starlight wrote:
> By the way what maximum penalty value can be refined by means of VMD's
> topology plugin ?
I'm sorry, I don't understand what you mean by this. I don't know "VMD's
topology plugin", but I doubt it can be used to obtain more reliable
values for penalties that are high. Please do have a look at my paper on
how the penalties are calculated.
> Here you can see 2 outputs with and without applied patch. As You can see
> the only defference is 1 extra bond when patch was used without any
> additions in dihedral terms. Does it correct in case of cyclic nucleotides?
Nope, the numbers after patching are not correct. AUTOGEN ANGLE DIHE is a
CHARMM command. It looks like your problem is that psfgen doesn't
recognize it, in which case you need to find the psfgen command that is
equivalent to AUTOGEN ANGLE DIHE .
Cheers,
Kenno.
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