1) I'm still curious about this, but don't feel you have to spend time
telling me about it if you have something that works.
2) & 3) Yay!
4) The names don't matter at all to AMBER. Suffixes are irrelevant to
how AMBER deals with the files. It can be more convenient to you,
when using certain programs, such as VMD, if you name the files so
that the program will recognize them. My favorite suffixes are .parm7
and .rst7. But others are fine, too. You can simply rename them
however you like.
On Sat, Aug 24, 2019 at 12:53 AM Rui Chen <rchen6.ualberta.ca> wrote:
>
> Dear Lachele,
>
> Thank you for your patience and help.
>
> 1. I used GLYCAM to generate the glycans first, however, I got severe
> steric clash in 2 out of 8 glycans.
> 2. I went to http://glycam.org/txt, checked the naming of the
> carbohydrate. My pdb file is correct ; ) It's very convenient to check the
> correct naming format of specific glycans.
> 3. I run minimization for the glycosylated protein, it worked fine. I think
> I am ok.
> 4. I generate a topology file and name if as .top, a coordinate file and
> name it as .crd, should I change them to .prmtop and .inpcrd, respectively?
> If yes, can I simply rename them?
>
> Thanks again and have a nice weekend.
>
> Best regards,
> Rui
>
>
> On Fri, Aug 23, 2019 at 6:59 AM Lachele Foley <lf.list.gmail.com> wrote:
>
> > 1. The easiest way is to build it using our online GUI here:
> > http://glycam.org/cb Another option is to enter DGlcpNAcb1-OME into
> > the box here: http://glycam.org/txt (note the http, not https -
> > this is one of the smaller reasons that the current version is being
> > retired soon.)
> >
> > 2. I'm guessing you didn't use our online builder to add glycans to
> > your protein (http://glycam.org/gp)? If you were using plain leap, I
> > would expect some geometric issues. There are currently no formats,
> > that we know of or can use, that will encode complex geometric
> > information such as one finds with carbohydrates. We are currently
> > working on encoding formats that will allow a system such as leap to
> > understand such complexities. For now, these need to be set manually
> > or by heuristics built in to software like our Glycoprotein Builder
> > GUI or CHARMM's.
> >
> > The force field is independent of the initial geometry. If an initial
> > geometry isn't terrible, a force field can be used to minimize the
> > system and improve the geometry. But, if the initial geometry is
> > really bad, a force field (generally) will not correct the issue.
> > This isn't a problem; to the contrary, it is desirable behavior. If,
> > in nature, you were to somehow place two atoms so close to each other
> > that their cores are very close to each other, the system would be
> > unstable. The force field only tries, incompletely, to mimic the
> > behavior of nature. The CHARMM gui is doing some geometric
> > manipulations for you in the background. With leap, you simply must
> > do them yourself.
> >
> > If leap built you a prmtop and inpcrd, you should be ok. But, run a
> > little simulation to be sure, of course.
> >
> > On Thu, Aug 22, 2019 at 10:21 PM Rui Chen <rchen6.ualberta.ca> wrote:
> > >
> > > 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
> > > >>
> > > >
> > > _______________________________________________
> > > 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
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Received on Mon Aug 26 2019 - 12:00:02 PDT
