Re: Protein-ligand simulation

From: Kenno Vanommeslaeghe (
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 .



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