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 Tue Apr 06 2021 - 14:30:02 PDT
