On Fri, Sep 23, 2011, David Condon wrote:
>
> I am attempting to load the new chi parameters by Zgarbová, et al. (J.
> Chem. Theory Comput., 2011, 7 (9), pp 2886–2902). I am following
> instructions on http://fch.upol.cz/en/rna_chi_ol/. I am pretty sure
> that the parameters loaded correctly, but I want to verify this before
> I invest 4 months in 12 simulations each :-)
A good check is just to use leaprc.ff10, which has these parameters, and uses
residue and atom names consistent with the current (version3) PDB standard.
>
> My input file, xleap.ol, is as follows:
>
> source /usr/local/amber/openmpi-intel/amber11/dat/leap/cmd/oldff/leaprc.ff99
> source /usr/local/amber/openmpi-intel/amber11/dat/leap/cmd/leaprc.ff99bsc0
> loadoff RNA_CI.lib
> loadamberprep all_nuc94_ol_bsc0.in
> loadamberparams frcmod.ol.dat
All of the above would be replaced with just "source leaprc.ff10"
> mol = loadpdb rna.caau.pdb
> solvateoct mol TIP3PBOX 8.65
> addions mol Na+ 0
> saveAmberParm mol prmtop inpcrd
> quit
>
> However, this produces the errors:
>
> 1)
> Warning: per-line charges being overridden by CHARGE block in
> D-ADENOSINE - with 5' - OH end group and 3' - O(minus)
You can look at the all_nuc94_ol_bsc0.in file, to verify that the same charges
are found on each atom line as in the CHARGE block that follows the residue.
But the warning is probably innocuous. [See also my suggestion about ff10...]
Other warnings you note also look innocuous, but try the simpler procedure,
making sure that the residue names in your PDB file are just "C", "A", "U",
etc. Note that a buffer region of only 8.6 Ang. is pretty small--are you sure
you don't want more waters?
....good luck...dac
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Received on Fri Sep 23 2011 - 13:30:03 PDT
