Dan,
that looks very cool and helpful, indeed!
And I saw that it is already included in the cpptraj documentation
within the Amber manual, great.
Many thanks for pointing this out to me!
Could you also comment briefly to my original question, i.e. is there
something like an automatic linkage detection for sugars already
implemented in leap and if so, what's its logic?
Best,
Anselm
Am 26.08.2022 um 15:54 schrieb Daniel Roe:
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Aug 26 2022 - 08:00:04 PDT
