Hi David,
Thanks for the prompt reply. I checked my prmtop file and indeed the atom
O4’ pops up instead of O4*. However, when I use the ambpdb command, O4*
pops up instead of O4’. Are there any ways to resolve this problem?
On Sat, Jan 25, 2014 at 10:08 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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--
Regards
Yip Yew Mun
Graduate, Masters
Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University
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Received on Fri Jan 24 2014 - 23:30:03 PST
