Re: Protein-ligand simulation

From: James Starlight (
Date: Tue Jun 25 2013 - 13:39:02 CDT


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 CY35 entry in the
latest charm 36 ff but I'm not sure if it reasonable to mix 27 parameters (
for protein) and 36 for ligand.

By the way does it possible to make refiriment of my cGMP (with big
penalties) with VMD plugins and make penalty estimation again?


2013/6/25 Kenno Vanommeslaeghe <>

> Hi James,
> On 06/25/2013 01:58 AM, James Starlight wrote:
>> Today I've used CGenFF at <> for my
>> test molecule (negatively charged cyclic guanosine mono phosphate).
> Actually, I forgot to mention CGenFF is not meant to be used for common
> biomolecules that are covered by the more specialized CHARMM force fields.
> cGMP is already in the CHARMM nucleic acid force field ( PRES CY35 ), so
> there's no force field assignment or optimization required whatsoever; all
> you need is a proper psf file. I could tell you how to generate it with the
> CHARMM program, but I'm not familiar with psfgen; the other denizens of
> this mailinglist may be able to help you out with that.
> How should I convert CGenFF output (str file) to the Namd par format ?
> In your case, it's better to use the nucleic acid force field, but just
> for future reference, NAMD actually uses the CHARMM parameter format (prm).
> Our str file is essentially a concatenated CHARMM topology (rtf) and prm
> file with some lines of "glue" around them. Both the rtf and prm sections
> start with a few lines starting with "*", and end with "END", so the
> "conversion" consists of copy-pasting the correct part of the str file to a
> separate file. Also note that an str file can be fed directly to NAMD - it
> will cleverly ignore everything but the parameter section.
> http://mackerell.umaryland.**edu/~kenno/cgenff/program.**html#namd>
> RESI tmp2.pdb -1.000 ! param penalty= 196.000 ; charge penalty=
>> 111.390
> It looks like in the case of this particular molecule, the penalties are
> woefully pessimistic. The penalties are by definition estimates, and we
> built in a little bit of systematic overestimation to err on the safe side.
> Because of this, one very occasionally encounters cases at the other tail
> of the bell curve where the penalties are unrealistically high, and this
> appears to be one of them. But again, using the nucleic acid force field
> for this one would still be preferable.
> Cheers,
> Kenno.

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