We are currently working on the inclusion of glycan processing in
PDB4AMBER. At the moment, its capabilities in that regard are a
little limited. Our biggest holdup right now is getting some graph
pattern matching to work. The latter will help make the atom renaming
robust even if some atoms are missing, etc. If you know anyone who
knows a lot about graph comparisons in the boost libraries, send them
to us! :-)
On Wed, Aug 21, 2019 at 7:02 PM Rui Chen <rchen6.ualberta.ca> wrote:
>
> Dear Lachele,
>
> I modified the PDB file according to the naming format you sent to me,
> there is no specific type for N, I guess it should be N2, no specific type
> for CT, I guess it should be CME. I changed them. Now in my leap.log file,
> I only got warning about improper torsion angles.
>
> It seems like it's better to delete all the H before running leap. Since
> PDB4AMBER will generate H, I removed all the H by VMD and then leap.
>
> I not not sure what's the exact purpose of PDB4AMBER, because for me I
> still need to manually modify everything.
> [image: Screen Shot 2019-08-21 at 4.29.20 PM.png]
>
> Thanks a lot for your help, very helpful.
>
> Best regards,
> Rui
>
> On Tue, Aug 20, 2019 at 11:32 PM Lachele Foley <lf.list.gmail.com> wrote:
>
> > > Thank you for the quick reply. Please let me know where can I find the
> > > naming templates.
> >
> > 0YB is in
> > http://glycam.org/docs/forcefield/wp-content/uploads/sites/6/2014/03/GLYCAM_06j-1.prep
> > Search the page to find the 0YB entry.
> >
> > NLN for mid-chain positions is in
> >
> > http://glycam.org/docs/forcefield/wp-content/uploads/sites/6/2014/02/GLYCAM_amino_06j_12SB.lib
> > Again, use a search to find that entry. I think your atoms are named
> > right in NLN, but didn't do a careful check. Leap will tell you all
> > about it if not.
> >
> > Both file formats are a little strange, but should be mostly readable.
> > More info on them is here: http://ambermd.org/formats.html
> > The first is a prep file and the second is an off file.
> >
> > > 1. By the way, PDB4AMBER generated the TER cards after each NLN, I can
> > > manually delete them.
> >
> > Ah. Leap will turn that residue and the next into their zwitterionic
> > forms if there is a TER card. Best to delete them. You might be
> > able to override that with some sort of leap instruction. I'm not
> > sure. Let me know if you have trouble after deleting them.
> >
> > > 2. NLN are 0YB are the correct naming. But as you can see in my leap
> > input
> > > file, I already source the force field specific for glycans. Now the only
> > > problem is the glycan.
> > > [image: Screen Shot 2019-08-20 at 10.23.18 PM.png]
> >
> > The 0YB *residue* is named correctly. It's the atoms that aren't.
> > For example, there are no atoms in the template named N, C, O, CT,
> > etc. I think NLN's atoms are ok.
> >
> > This is also the issue with the hydrogens. They all have to be named
> > correctly or leap fails.
> >
> > > 3. I used PDB2PQR to predict the protonation states of the protein,
> > PDB2PQR
> > > generates the hydrogens. I manually deleted all the hydrogens. Does it
> > > influence the protonation state of the protein?
> >
> > I suppose you're talking about histidine residues? So long as you've
> > named them for the protonation state you want (HID, HIE or HIP), leap
> > should add in the correct number of hydrogens and assign reasonable
> > partial charges to them. I didn't find any instances of "HIS" in your
> > file, but I did find HID and HIE, so I think you're ok.
> >
> >
> >
> > > On Tue, Aug 20, 2019 at 10:07 PM Lachele Foley <lf.list.gmail.com>
> > wrote:
> > >
> > > > Hi!
> > > >
> > > > You shouldn't use TER cards after the NLNs unless they are actually at
> > > > the end of an amino acid chain. They are amino acid (modified), and
> > > > don't follow the glycan rules.
> > > >
> > > > Removing hydrogens isn't necessary, but their names need to exactly
> > > > match the templates in the force fields. Folks usually prefer to just
> > > > remove them rather than rename them all. If any of their positions
> > > > are critical, leave those in and make sure the names are right.
> > > > Otherwise, it's easier to delete them. Or rename them all if you
> > > > prefer to do that.
> > > >
> > > > Your NLN and 0YB atom names need to exactly match the templates as
> > > > well. The same hydrogen-naming logic applies, but you must ensure
> > > > that the heavy-atom names match.
> > > >
> > > > Do you know how to find the lib and prep files where the templates are
> > > > (for naming)?
> > > >
> > > > On Tue, Aug 20, 2019 at 11:49 PM Rui Chen <rchen6.ualberta.ca> wrote:
> > > > >
> > > > > By the way, should I remove all the hydrogens before using PDB4AMBER
> > and
> > > > > why? Thank you.
> > > > >
> > > > > On Tue, Aug 20, 2019 at 9:43 PM Rui Chen <rchen6.ualberta.ca> wrote:
> > > > >
> > > > > > Hello,
> > > > > >
> > > > > > I am preparing a PDB file for running LEaP. Since I add glycans
> > using
> > > > > > CHARMM GUI, I rename the glycans to NLN (N-linkages to ASN)
> > according
> > > > to
> > > > > > AMBER manual (LEaP). However, I got error when I run leap. I
> > changed
> > > > the
> > > > > > TER cards, but it still didn't work. I also checked the connections
> > > > between
> > > > > > the carbohydrates and the ASN amino acids using VMD, I couldn't
> > find
> > > > > > anything wrong. The leap input file, log file, pdb file (mentioned
> > in
> > > > leap
> > > > > > input file) are attached.
> > > > > >
> > > > > > Could you please give me some clue about how to solve the problem?
> > > > Looking
> > > > > > forward to hearing from you.
> > > > > >
> > > > > > Sincerely,
> > > > > > Rui
> > > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > >
> > > >
> > > > --
> > > > :-) Lachele
> > > > Lachele Foley
> > > > CCRC/UGA
> > > > Athens, GA USA
> > > >
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> > > >
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> >
> >
> >
> > --
> > :-) Lachele
> > Lachele Foley
> > CCRC/UGA
> > Athens, GA USA
> >
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> >
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Wed Aug 21 2019 - 19:00:02 PDT
