Dear Vaibhav,
Just a follow up suggestion... you can directly visualize the .prmtop and .inpcrd (load it as "rst7") files in VMD [
https://www.ks.uiuc.edu/Research/vmd/]... there is no need to generate a PDB file with connectivity to see the actual bond links, VMD reads them from the AMBER topology without guessing...
Best,
Matias
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[pasteur.uy/en/labs/biomolecular-simulations-laboratory/]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "David Case" <david.case.rutgers.edu>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Viernes, 31 de Mayo 2019 21:57:39
Asunto: Re: [AMBER] error with loading HEM parameters for constph redox calcuations
On Fri, May 31, 2019, Vaibhav Dixit wrote:
>I created a pdb with connectivity info from prmtop/inpcrd using ambpdb
>command and it shows expected bonds in pymol.
Don't rely (just) on pymol and ambpdb connecctivity. Learn to use
parmed's printBonds command to make sure what bonds are present (or
missing) from the prmtop file.
>It will be still helpful if someone could explain the meaning of the
>message tleap is giving about "*Residues lacking connect*".
An ordinary protein or DNA residue has "head" and "tail" connections,
telling which atoms are use to bond to the previous and following
residues. Residues (like WAT) that aren't part of a polymer are missing
those connections. An N-terminal amino acid will have only a tail
connection, since there is no previous residue. You CYP residue should
have both head and tail, since it is to be a part of a polypeptide
chain.
This information probably should not be in the tleap output, since it is
only *very* occasionally useful, and you can always just look at the
.lib or .off file (or use the desc command in tleap) to find out this
information. But it's been there for three decades, taking up space....
...dac
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Received on Mon Jun 03 2019 - 16:30:02 PDT
