On Mon, Oct 03, 2011, Asmita Gupta wrote:
> > >
> > > FATAL: Atom .R<RG5 1>.A<H02' 33> does not have a type.
In your pdb file, the hydroxyl protons are identified as "H-zero-2-prime",
whereas they need to be "HO2'", with the letter "O" as the second character.
[Let us know if it was an Amber program that made this pdb file!]
You also have a "extra" phosphate group at the 5' end of the chain. First,
be sure you really want that group. If you do, you first have to figure out
what charge you want it to have. If you want this to be a 2- phosphate, you
will have to construct a special residue for that, since it would not be a
part of the standard Amber library. If having it be -1 is OK, then you would
need to use some graphics program (xleap would work), to create an initial
position for the missing OH group. Copy those coordinates to the start of
each chain, and use "OHE" for the residue name. (Use the "desc" command to
give details about the OHE residue). Double check that total charge is
correct....I've never done this myself, so I'm just giving a general overview
of what is needed.
...dac
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Received on Mon Oct 03 2011 - 12:00:02 PDT
