Hi Gustavo,
Welcome to the ordeal that is trying to get LEaP to work with sugars.
I've recently butted my head up against this myself. I have a
work-in-progress command in cpptraj called 'prepareforleap' that I've
been testing that tries to make this process a bit easier. It will
disconnect any sugars, try to rename them properly, and write out the
leap input needed to recreate the bonds after you load the prepared
structure into leap (it also creates leap input to bond disulfides and
changes CYS to CYX etc). Again, it's still a work in progress so it
may not work for your system. If you are feeling brave and want to
give it a shot, email me off-list and I'll give you more details.
-Dan
On Tue, Apr 6, 2021 at 5:27 PM Gustavo Seabra <gustavo.seabra.gmail.com> wrote:
>
> 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 - 08:00:02 PDT
