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 - 06:00:04 PDT
