See comments below...
> Few issues are, should not I have to include the library file for
> AMBER99CHI force field (all_RNA_YST.lib) after the command
> " loadamberparams frcmod.parmCHI" !
For your system, no. You only have one mononucleoside system, which is
a s2U residue solvated with water. all_RNA_YST.lib is the library file for
all regular RNA residues (uridine, cytidine, guanosine, adenosine). It is
similar to all_nucleic94.lib except for one atom type (C6 of pyrimidines
and C8 of purines).
> I found that with the s2U geometry remains OK during simulation (checked in
> VMD). The problem to get new the angular and and torsional terms, as I am
> using the parameters for s2U developed by others (Santa Lucia et al.). Then
> I have to optimize the system.
Take a look at the following paper we published in 2010.
Yildirim, I., Stern, H. A., Kennedy, S. D., Tubbs, J. D., and Turner, D.
H., “Re-parameterization of RNA χ torsion parameters for the AMBER force
field and comparison to NMR spectra for cytidine and uridine”, J. Chem.
Theory and Comput. 6, 1520-1531, 2010.
> What is the logic behind all these ? As I understood when we use the
> command "loadamberparams frcmod.parmCHI", it is converting the par99 into
> parm99chi, after that when i am using the commands "loadamberparams
> 2SU.frcmod" and "loadamberprep 2SU.prepin", the parm99chi force field is
> applying on s2U. Am I correct ?
The logic is the following: When you load a parameter set (such us
frcmod.parmCHI) it will either load the new parameter sets or re-write the
old parameter sets. In frcmod.parmCHI case, it loads the new chi parameter
sets for RNA residues (defined in all_RNA_YST.lib). The new atom types
defined in frcmod.parmCHI are C1,C2,C3,C4. And without calling
all_RNA_YST.lib in leap, you will not be able to use this new chi
torsional parameters for RNA. Check out the atom types defined for atom
name C6 in pyrimidines and atom name C8 in purines (compare
all_RNA_YST.lib and all_nucleic94.lib). They are different.
If I am not mistaken, SantaLucia created a library for modified residues.
The only parameterization his group did was on calculating the RESP
charges for these molecules. He did not do any chi revision
(re-parameterization) for these molecules. It assumes that the chi
parameters of these molecules are similar to RNA residues. Can RNA CHI
parameters mimic the potential energy surfaces (around chi) for these
modified residues? Probably not, but it is also possible that it will not
make a big difference (whether using the RNA chi torsional parameters for
these molecules or revising the chi torsions for each modified residue).
In 2SU case, the atom type of atom C6 is CM (if I am not mistaken. I dont
have your files anymore). Check out your .prepi file of 2SU. If you use
atom type CM for atom name C6 in 2SU, it will use the old chi parameters
and I would not suggest you to use those parameters. Re-create your .prepi
file and only change the atom type for atom name C6 to 'C4'. In this case,
after loading frcmod.parmCHI, you will be able to use the revised chi
parameters. Or the best would be to re-parameterize the chi for 2SU.
> Santa Lucia et al. group instructed for their parameter for s2U for parm99,
> in the following way:
>
> source oldff/leaprc.rna.ff99
> loadamberparams 2SU.frcmod
> loadamberprep 2SU.prepin
This is right, but it will not use the revised chi parameters. You need to
change the atom type in 2SU.prepin.
By the way, when I looked at 2SU.frcmod before, there were a lot of
parameters defined. The only difference between 2SU and uridine is the
mutation of O2 to S2, which should not require you to define too many new
parameters.
Ilyas,
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Received on Mon Dec 17 2012 - 04:00:05 PST
