On Wed, Apr 20, 2011, mish wrote:
> once again a small problem. After making the bond when I write the PDB file
> by-
> savapdb lig lig_tleapout.pdb
> The lig_tleapout.pdb file has both the residues separated by TER.
You probably want a TER card there, although it is optional. Whether or not
"tleap makes a bond in reality" is determined by the prmtop file it writes,
not the pdb file.
> Yes I can see the bond in
> VMD when i load *.prm and *.crd file written by tleap
Then the bond *is* there. You can double-check if you like by using the
rdparm program to list all the bonds in your prmtop file.
> but why doesnt tleap
> writes molecule as one molecule as residue number 1 and 2.
The use of the "TER" card in pdb files is rather mysterious and not completely
consistent. "Real" PDB files will generally make ligands be "HETATM" cards,
and will put a TER card between the ATOM cards and the HETATM cards, but will
*not* put TER cards between different HETATM groups that are not bonded to
each other.
Amber doesn't really follow this convention very closely, and I guess that is
more a bug than a feature. Amber tends to put TER cards between molecules,
and to not distinguish HETATMs from ATOMs. This could/should be fixed in
future versions, although a general way to know what is an ATOM and what is a
HETATM is not all that clear in some cases. Remember that is it what is in
the prmtop file that "counts": pdb files are provided just to help communicate
with other programs.
...dac
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Received on Wed Apr 20 2011 - 10:30:03 PDT
