On Jan 25, 2014 7:39 AM, "David A Case" <case.biomaps.rutgers.edu> wrote:
>
> 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 Sat Mar 15 2014 - 21:00:03 PDT
