On Sat, Jan 25, 2014, Yip Yew Mun wrote:
> Hi, I was running the command ‘distance’ in ptraj between some atoms
> from the protein to DNA. Surprisingly, the atom O4* can’t be read but
> O4’ can. Also, some atoms of the protein residues such as NZ of lysine
> can be read on some lysine residues but not others. Is this a bug?
First, see if changing to cpptraj helps.
If you built the DNA with any of the recent libraries, there won't be an
O4* atom, since that name was changed to O4' a long time ago. Look at your
prmtop file to see the atom names that are there.
I'm guessing that the lysine problem is (much) more likely to be something
inconsistent between the input and the prmtop file than to be a bug in the
program. Double-check your inputs vs the prmtop, and simplify things as
much as possible, to see if you can find the problem.
...dac
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Received on Fri Jan 24 2014 - 18:30:02 PST
