On Fri, Oct 16, 2015, Robert Molt wrote:
> I assume that the
> name "1W5" ahead of the .frcmod file indicates that a defined unit "1W5"
> from the previous step gets those parameters?
No. First, the file names have no meaning to LEaP; only the content of the
files is used. So, you could rename the file as "abracadabra" if you want.
Second, parameters are global: the are (typically) read in as a parm.dat file,
followed by zero or more frcmod files. If there are duplicate parameters, the
ones loaded later replace the one loaded earlier. All parameters potentially
apply to all units (residues).
> WARNING: The unperturbed charge of the unit: -30.000006 is not zero.
As I read your email, you have 15 phosphate groups in each chain, each with a
charge of -1, so the above looks to be correct.
> I believe that there are 2 more negative charges at the 5' ends,
This not correct.
>
> If this is the nature of the problem, the solution is clear (I change
> the OH in my .ac file to a OS).
Sounds right to me....give it a try. Easiest to just edit the final prepin
file than to back to some antechamber intermediate file.
> If this is true, a corollary is that I have to change all the parameters
> of the OH, manually, to be what they are for an OS?
If you change the atom type to OS, then it will be assigned parameters
appropriate for OS. It sounds like you just have to make one minor edit,
changing the type of one atom in the prepin file.
....dac
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Received on Fri Oct 16 2015 - 18:30:02 PDT
