Re: Protein-ligand simulation

From: JC Gumbart (
Date: Wed Jun 26 2013 - 15:21:09 CDT

psfgen autogenerates by default when building segments (but not patches!). The closest equivalent would be to add near the end of the script before writing out the psf:

regenerate angles dihedrals

On Jun 26, 2013, at 3:07 PM, Kenno Vanommeslaeghe wrote:

> 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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