Dear Lachele,
1. Where can I download the library for GlcpNAcb1-OME?
2. I used CHARMM GUI to generate the glycans, now I am running Amber, in
the leap input file, I sourced the GLYCAM force field, even though it
worked, I think that's not correct. The reason I use CHARMM GUI to generate
the glycans not GLYCAM is that I tried to use GLYCAM to generate the
glycans, I got severe steric clash, CHARMM GUI worked fine and easier. Do
you have any suggestion about the force field?
Best regards,
Rui
On Thu, Aug 22, 2019 at 9:45 AM Rui Chen <rchen6.ualberta.ca> wrote:
> Thank you for your help. Where can I download the library
> for GlcpNAcb1-OME? I couldn't find it.
>
>
>
> On Thu, Aug 22, 2019 at 8:24 AM Lachele Foley <lf.list.gmail.com> wrote:
>
>> 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
>> > > > > > >
>> > > > > > _______________________________________________
>> > > > > > 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
>> > > > >
>> > > > _______________________________________________
>> > > > 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
>> > >
>> > _______________________________________________
>> > 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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Received on Thu Aug 22 2019 - 19:30:02 PDT
