1. Probably. The only way to be certain is to download a
GlcpNAcb1-OME from our site and open them both up in VMD/Chimera/etc
and compare the atoms to each other and assign names based on that
comparison. I think you also need to change C to C2N and O to O2N.
2. Yes.
3. If all goes according to plan, yes. If this is not what happens,
then something went wrong. The NAc group in GlcNAc is often a little
bent in PDB files.
On Wed, Aug 21, 2019 at 10:18 PM Rui Chen <rchen6.ualberta.ca> wrote:
>
> No problem.
> Just want to double check:
> 1. I renamed N to N2, CT to CME, that's correct.
> 2. In order to avoid the problem of hydrogen naming, I delete all the
> hydrogens, since leap will generate the hydrogens for me.
> 3. I don't need to worry about the improper torsions, minimization will
> solve the problem.
> Thank you.
>
> On Wed, Aug 21, 2019 at 7:36 PM Lachele Foley <lf.list.gmail.com> wrote:
>
> > 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
> > > > > >
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > > _______________________________________________
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> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > >
> > > >
> > > > --
> > > > :-) Lachele
> > > > Lachele Foley
> > > > CCRC/UGA
> > > > Athens, GA USA
> > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
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> >
> >
> >
> > --
> > :-) Lachele
> > Lachele Foley
> > CCRC/UGA
> > Athens, GA USA
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Thu Aug 22 2019 - 07:30:02 PDT
