Dear Gustavo,
mmm... that seems a pitfall in the AMBER's pipeline...
Most probably CONNECT records from your original PDB are useless due to the re-ordering of atoms after the former leap...
*** SPOILER ALERT: The following is an untrusted workaround ****
I'm guessing here, but if the issue is the PDB format, then you can try saving the coordinates in .cif, which leap is able to read...
But the problem could be leap setting bonds from both .lib (automatically) and from CONNECT, duplicating bonds and hence giving an error of "too many bonds"... if that's the case, you can try removing all bonds from residues and connection between amino acids in the topology (leaving glycosidic bonds untouched) by using the command "change removebonds" in cpptraj (note: this may also eliminate S-S bridges)... then you can save the PDB with CONNECT records...
Hope this helps...
Best,
MatÃas
------------------------------------
PhD.
Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay
[
http://pasteur.uy/en/labs/biomolecular-simulations-laboratory]
[
http://www.sirahff.com]
----- Mensaje original -----
De: "Gustavo Seabra" <gustavo.seabra.gmail.com>
Para: "AMBER Mailing List" <amber.ambermd.org>
Enviados: Martes, 6 de Abril 2021 18:26:19
Asunto: [AMBER] Add molecule to prmtop/inpcrd ?
Hi all,
I wonder if there's any way to add a molecule to previously prepared
prmtop/inpcrd pair, without using any intermediate file (pdb, etc.)
Can parmed do that?
The reason I ask:
I did a simulation of a reasonably large system, with a membrane-inserted
glycosylated protein. Now, I'd like to add a ligand to a specific frame
from the trajectory I obtained, and run a new simulation in the presence of
this ligand.
I tried the obvious: use cpptraj to select the frame, write as PDB, add the
ligand and use LEaP again to build the new system, but the problem is that
the new PDB saved by cpptraj either does not have CONECT information, or
has it for ALL bonds. (The same happens with AMBPDB). If I write with NO
CONECT, LEaP then doesn't read the glycam bonds correctly. If write the
CONECT cards, LEaP gets confused with some atoms having too many bonds
(apparently it may be caused by numbers overlapping in the PDB format)
Thanks,
--
Gustavo Seabra.
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Received on Wed Apr 07 2021 - 07:00:02 PDT
