Re: Protein-ligand simulation

From: James Starlight (jmsstarlight_at_gmail.com)
Date: Tue Jun 25 2013 - 13:39:02 CDT

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 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?

James

2013/6/25 Kenno Vanommeslaeghe <kvanomme_at_rx.umaryland.edu>

> Hi James,
>
> On 06/25/2013 01:58 AM, James Starlight wrote:
>
>> Today I've used CGenFF at paramchem.org <http://paramchem.org/> 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
>> GROUP ! CHARGE CH_PENALTY
>>
>
> 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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