Re: Protein-ligand simulation

From: James Starlight (
Date: Wed Jun 26 2013 - 00:56:38 CDT


thanks again for the explanation!

By the way what maximum penalty value can be refined by means of VMD's
topology plugin ?

Also I'll be thankful if some one helps me with psfgen

Using my CGMP mollecule sas the input and charm 36 params I've generated
topology (using GUA and PRESS CY35 entries). Below you can find my script
where I applied CY35 patch on A:1 which is the my whole cgmp molecule. I'm
not quite sure here if I should define both joined atoms explicitly here
(in that case O3' and P)

package require psfgen
topology top_all36_na.rtf
segment A {
pdb input.pdb
first NONE
last NONE
coordpdb input.pdb A

patch CY35 A:1

writepsf ligand.psf
writepdb ligand.pdb

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?
# no path
psfgen) total of 34 atoms
psfgen) total of 36 bonds
psfgen) total of 62 angles
psfgen) total of 92 dihedrals
psfgen) total of 3 impropers
psfgen) total of 0 cross-terms

# patch applied
psfgen) total of 34 atoms
psfgen) total of 37 bonds
psfgen) total of 62 angles
psfgen) total of 92 dihedrals
psfgen) total of 3 impropers
psfgen) total of 0 cross-terms


2013/6/25 Kenno Vanommeslaeghe <>

> Hi James,
> On 06/25/2013 02:39 PM, James Starlight wrote:
>> Kenno,
>> thank you again for such detailed explanations!
>> Unfortunately I didnt find parameters for cyclic nucleotides in the
>> charm27 param files (I've looked for it in the par_all27_na.prm and
>> par_all27_na.inp ) Perhaps I should look for the PRES CY35entry in the
>> latest charm 36 ff but I'm not sure if it reasonable to mix 27 parameters
>> ( for protein) and 36 for ligand.
> - Yes, I was looking at the CHARMM36 NA force field.
> - Technically spoken, cyclic nucleotides don't need special parameters,
> though chemically spoken, the use of the non-cyclic parameters must be
> validated. The presence of the intra-nucleotide cyclization patch in
> CHARMM36 suggests that's been done (for CHARMM36 at least).
> - I don't think it would be a huge problem to mix the CHARMM36 NA force
> field with the CHARMM22 protein force field because there are few nonbonded
> changes, but is there any reason you can't use the CHARMM36 protein force
> field? It can be freely downloaded from the MacKerell web site, and is
> supposed to be a drop-in replacement and a significant improvement over
> - By the way, there does not exist a CHARMM27 protein force field.
> By the way does it possible to make refiriment of my cGMP (with big
>> penalties) with VMD plugins and make penalty estimation again?
> Nope. Assuming the optimization went well and the resulting charges and
> parameters look physical, the only way to get an idea of the quality of
> *optimized* parameters is to run experimental validation.
> See also the following paper for details on how the penalties are
> calculated:
> K. Vanommeslaeghe, E. P. Raman, A. D. MacKerell Jr., J. Chem. Inf. Model.
> 2012, 52, 3155-3168.
> Cheers,
> Kenno.

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