AMBER Archive (2005)

Subject: Re: AMBER: ambpdb TER problems

From: David A. Case (case_at_scripps.edu)
Date: Tue Dec 27 2005 - 14:30:48 CST

On Tue, Dec 27, 2005, Sam wrote:
>
> Indeed, it turns out that the ambpdb-misplacement of TER card
> only happens after I have solvated the structure. Curious.. This
> is independent of whether or not I have added K+ ions to the
> structure (or in which order I do these two steps).

Here is what I think is a resolution of this problem:

First, it is not a bug with ambpdb: the prmtop file is wrong. Look for the
section labelled ATOMS_PER_MOLECULE, and you will see that the information is
not quite right there. ambpdb uses this information to put in TER cards.
[The reason things "work" without solvation is that LEaP only creates
molecule information for periodic simulations. So for non-periodic stuff,
ambpdb has to figure out what the molecules are on its own, and it does that
correctly.]

Second, the problem arises from the FS4 group. Because of the CONECT records
at the bottom of the pdb file, LEaP is (correctly) treating the FS4 group as a
part of the first molecule (the protein). But it doesn't know how to put the
FS4 coordinates up with the first molecule. This is not going to be easy to
fix in general, but here is the workaround:

Move the HETATM records of the FS4 group (in the protein.pdb file) to the top
of the file (either before or after the protein). I think the CONECT records
will all still work correctly, but please double check the connectivities
(e.g.: I get the FE4 should be bonded to CYS 214 -- make sure that is
correct.) Then you should be able to use the other commands you have already
been using.

Basically, each "molecule" needs to have contiguous coordinates in the input
pdb file. Having the DNA strands in between the protein and its covalently
linked atoms confuses LEaP. It is unlikely that this restriction will go away
any time soon. The notion that each molecule has contiguous coordinates
is pretty deeply embedded into the Amber codes; but we might be able to at
least get LEaP to check for violations of this requirement and to issue an
error message; but that is all for the future.

...thanks for the report....dac

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