Hi,
You might want to try the 'prepareforleap' command in cpptraj, which
is designed to take a PDB and provide a tleap-readable PDB plus all
the leap input needed to set it up properly. You can find an example
here: https://github.com/Amber-MD/cpptraj/tree/master/examples/prepareforleap/NIST-mAb
The manual entry has full details on the command (there is also an
Amber-Hub entry here: https://amberhub.chpc.utah.edu/prepareforleap/).
There is also an accompanying paper:
https://onlinelibrary.wiley.com/doi/10.1002/jcc.26847
Hope this helps,
-Dan
On Fri, Aug 26, 2022 at 8:36 AM Dr. Anselm Horn via AMBER
<amber.ambermd.org> wrote:
>
> Dear Amber users and developers,
>
> some time ago, I tried to setup a protein system bound to a branched
> glycan and ran into trouble with tleap.
>
> Following the principles described in the Amber manual section 13.7.3.2.
> "Example: Adding a branched glycan to 3RN3 (N-linked glycosylation)" I
> added TER cards between all entities (protein chains and single sugar
> residues) in the input pdb and then tried to create all bonds between
> the glycan system manually with explicit bond commands in tleap.
>
> However, tleap complained with the following error message:
>
> !FATAL ERROR----------------------------------------
> !FATAL: In file [unitio.c], line 1808
> !FATAL: Message: 1-4: cannot add bond 22324 22325
> This may be caused by duplicate bond specifications;
> for example, explicit bond commands in addition to PDB conect records.
> !
> !ABORTING.
>
> Deleting all the bond commands made the error message vanish, but left
> my system without the correct topology, of course.
>
> Using the desc command, I tried to elucidate the bond situation at the
> atoms of interest of all the sugar moieties. It seemed to me that
> sometimes bonds between sugars were created automatically; this feature
> were nice for linear glycans, but may be troublesome for branched ones,
> if no information is printed out, since the situation is not as clear as
> it is for a linear peptide sequence.
>
> Thus I wanted to ask, whether my observation was right and there is
> something like an automatic linking feature for glycan residues in leap,
> and whether there is a description about that in the manual.
>
> If such a feature exists, my suggestion to the developers is to add a
> simple user info when a bond is added between atoms in sugars - it may
> also be a nice idea to have a similar comment printed out after each
> successfully issued bond command in tleap in general, i.e. between which
> atoms a link was established. An alternative would be a keyword that
> turns off automatic (glycan) residue linking, but that may be harder to
> implement.
>
> However, since the system was a rather complex one, it could be that I
> am wrong and made a mistake somewhere else or used a tleap program from
> an earlier Amber version.
> (In the meantime, this system has been setup correctly...)
>
> Best regards,
>
> Anselm
>
> Bioinformatik | NHR.FAU
> Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)
> Germany
>
>
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Received on Fri Aug 26 2022 - 07:00:16 PDT
