Date: Wed, 21 Aug 2019 17:02:22 -0600
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
> > > > >
> > > > _______________________________________________
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> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> > >
> > > --
> > > :-) Lachele
> > > Lachele Foley
> > > CCRC/UGA
> > > Athens, GA USA
> > >
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> > > AMBER.ambermd.org
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> > >
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>
>
>
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
>
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