Hello Dr. Case,
thank you very much for your help!
I appreciate it!
-Dave
On Fri, Sep 23, 2011 at 4:10 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> 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 Sun Sep 25 2011 - 14:30:03 PDT
