On Wed, Apr 21, 2021, Suchetana Gupta wrote:
>I have a protein where I have a modified amino acid residue beta hydroxy
>aspartic acid. It is written as BHD in our PDB file.
>However, the output PDB file has a TER
>cut before and after the modified residue, although the starting file did
>not have it.
This probably means that you don't have the "head" and "tail" connections
set correctly in your off file for the modified residue. If that is the
case, then tleap doesn't know to create bonds to the residues before and
after the BHD. (You can check this is the printBonds action in ParmEd,
looking to see if the bonds are there in the prmtop file.)
The ambpdb result is just a symptom of the underlying error: since the BHD
(probably) has no bonds to neighboring residues, ambpdb treats BHD as a
separate molecule, put TER cards in. Other errors, like this one, arise
from the same original problem:
>Error: Atom 1015 was assigned a lower molecule # than previous atom.
>Error: This can happen if bond information is incorrect or missing
If this is a one-off calculation, you could just use the bond command in
tleap to add the needed bonds. Better would be to use the "set" command in
tleap to set the head and tail atoms in your modified residue, save the
results, then re-run tleap.
...good luck...dac
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Received on Wed Apr 21 2021 - 09:00:02 PDT
