It should be ok to ignore those warnings. VMD just doesn't know much
about glycoproteins yet. :-)
On Fri, Aug 30, 2019 at 5:38 PM Rui Chen <rchen6.ualberta.ca> wrote:
>
>
> Dear Lachele,
> Please find attached my tleap input file. I generated the coordinate file
> and topology file with tleap. When I load the topology file into VMD, I got
> the following error. All the warnings are about the connections between ASN
> and glycans. I checked the connections are correct, can I ignore the
> warnings?
> Best regards,
> Rui
> Screen Shot 2019-08-30 at 3.37.15 PM.png
>
> On Mon, Aug 26, 2019 at 1:23 PM Rui Chen <[1]rchen6.ualberta.ca> wrote:
>
> Dear Lachele,
> Got it.Â
> Thank you for your help.
> Best regards,
> Rui
>
> On Mon, Aug 26, 2019 at 12:31 PM Lachele Foley <[2]lf.list.gmail.com> wrote:
>
> 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)Â 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 <[3]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 [4]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 <[5]lf.list.gmail.com>
> wrote:
> >
> > > 1. The easiest way is to build it using our online GUI here:
> > > [6]http://glycam.org/cb  Another option is to enter DGlcpNAcb1-OME
> into
> > > the box here: [7]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 ([8]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 <[9]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 <[10]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
> <[11]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
> <[12]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
> <[13]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
> <[14]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 <
> > > [15]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
> > > > >> > > > >
> > > > >> > >
> > > > >>
> > >
> [16]http://glycam.org/docs/forcefield/wp-content/uploads/sites/6/2014/03/G
> LYCAM_06j-1.prep
> > > > >> > > > > Search the page to find the 0YB entry.
> > > > >> > > > >
> > > > >> > > > > NLN for mid-chain positions is in
> > > > >> > > > >
> > > > >> > > > >
> > > > >> > >
> > > > >>
> > >
> [17]http://glycam.org/docs/forcefield/wp-content/uploads/sites/6/2014/02/G
> LYCAM_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:Â
> [18]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.Â
> 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 <
> > > > >> [19]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 <
> > > [20]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 <
> > > > >> [21]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
> > > > >> > > > > > > > [22]AMBER.ambermd.org
> > > > >> > > > > > > > [23]http://lists.ambermd.org/mailman/listinfo/amber
> > > > >> > > > > > >
> > > > >> > > > > > >
> > > > >> > > > > > >
> > > > >> > > > > > > --
> > > > >> > > > > > > :-) Lachele
> > > > >> > > > > > > Lachele Foley
> > > > >> > > > > > > CCRC/UGA
> > > > >> > > > > > > Athens, GA USA
> > > > >> > > > > > >
> > > > >> > > > > > > _______________________________________________
> > > > >> > > > > > > AMBER mailing list
> > > > >> > > > > > > [24]AMBER.ambermd.org
> > > > >> > > > > > > [25]http://lists.ambermd.org/mailman/listinfo/amber
> > > > >> > > > > > >
> > > > >> > > > > > _______________________________________________
> > > > >> > > > > > AMBER mailing list
> > > > >> > > > > > [26]AMBER.ambermd.org
> > > > >> > > > > > [27]http://lists.ambermd.org/mailman/listinfo/amber
> > > > >> > > > >
> > > > >> > > > >
> > > > >> > > > >
> > > > >> > > > > --
> > > > >> > > > > :-) Lachele
> > > > >> > > > > Lachele Foley
> > > > >> > > > > CCRC/UGA
> > > > >> > > > > Athens, GA USA
> > > > >> > > > >
> > > > >> > > > > _______________________________________________
> > > > >> > > > > AMBER mailing list
> > > > >> > > > > [28]AMBER.ambermd.org
> > > > >> > > > > [29]http://lists.ambermd.org/mailman/listinfo/amber
> > > > >> > > > >
> > > > >> > > > _______________________________________________
> > > > >> > > > AMBER mailing list
> > > > >> > > > [30]AMBER.ambermd.org
> > > > >> > > > [31]http://lists.ambermd.org/mailman/listinfo/amber
> > > > >> > >
> > > > >> > >
> > > > >> > >
> > > > >> > > --
> > > > >> > > :-) Lachele
> > > > >> > > Lachele Foley
> > > > >> > > CCRC/UGA
> > > > >> > > Athens, GA USA
> > > > >> > >
> > > > >> > > _______________________________________________
> > > > >> > > AMBER mailing list
> > > > >> > > [32]AMBER.ambermd.org
> > > > >> > > [33]http://lists.ambermd.org/mailman/listinfo/amber
> > > > >> > >
> > > > >> > _______________________________________________
> > > > >> > AMBER mailing list
> > > > >> > [34]AMBER.ambermd.org
> > > > >> > [35]http://lists.ambermd.org/mailman/listinfo/amber
> > > > >>
> > > > >>
> > > > >>
> > > > >> --
> > > > >> :-) Lachele
> > > > >> Lachele Foley
> > > > >> CCRC/UGA
> > > > >> Athens, GA USA
> > > > >>
> > > > >> _______________________________________________
> > > > >> AMBER mailing list
> > > > >> [36]AMBER.ambermd.org
> > > > >> [37]http://lists.ambermd.org/mailman/listinfo/amber
> > > > >>
> > > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > [38]AMBER.ambermd.org
> > > > [39]http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> > >
> > > --
> > > :-) Lachele
> > > Lachele Foley
> > > CCRC/UGA
> > > Athens, GA USA
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > [40]AMBER.ambermd.org
> > > [41]http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > [42]AMBER.ambermd.org
> > [43]http://lists.ambermd.org/mailman/listinfo/amber
> --
> :-) Lachele
> Lachele Foley
> CCRC/UGA
> Athens, GA USA
> _______________________________________________
> AMBER mailing list
> [44]AMBER.ambermd.org
> [45]http://lists.ambermd.org/mailman/listinfo/amber
>
> References
>
> 1. mailto:rchen6.ualberta.ca
> 2. mailto:lf.list.gmail.com
> 3. mailto:rchen6.ualberta.ca
> 4. http://glycam.org/txt
> 5. mailto:lf.list.gmail.com
> 6. http://glycam.org/cb
> 7. http://glycam.org/txt
> 8. http://glycam.org/gp
> 9. mailto:rchen6.ualberta.ca
> 10. mailto:rchen6.ualberta.ca
> 11. mailto:lf.list.gmail.com
> 12. mailto:rchen6.ualberta.ca
> 13. mailto:lf.list.gmail.com
> 14. mailto:rchen6.ualberta.ca
> 15. mailto:lf.list.gmail.com
> 16. http://glycam.org/docs/forcefield/wp-content/uploads/sites/6/2014/03/GLYCAM_06j-1.prep
> 17. http://glycam.org/docs/forcefield/wp-content/uploads/sites/6/2014/02/GLYCAM_amino_06j_12SB.lib
> 18. http://ambermd.org/formats.html
> 19. mailto:lf.list.gmail.com
> 20. mailto:rchen6.ualberta.ca
> 21. mailto:rchen6.ualberta.ca
> 22. mailto:AMBER.ambermd.org
> 23. http://lists.ambermd.org/mailman/listinfo/amber
> 24. mailto:AMBER.ambermd.org
> 25. http://lists.ambermd.org/mailman/listinfo/amber
> 26. mailto:AMBER.ambermd.org
> 27. http://lists.ambermd.org/mailman/listinfo/amber
> 28. mailto:AMBER.ambermd.org
> 29. http://lists.ambermd.org/mailman/listinfo/amber
> 30. mailto:AMBER.ambermd.org
> 31. http://lists.ambermd.org/mailman/listinfo/amber
> 32. mailto:AMBER.ambermd.org
> 33. http://lists.ambermd.org/mailman/listinfo/amber
> 34. mailto:AMBER.ambermd.org
> 35. http://lists.ambermd.org/mailman/listinfo/amber
> 36. mailto:AMBER.ambermd.org
> 37. http://lists.ambermd.org/mailman/listinfo/amber
> 38. mailto:AMBER.ambermd.org
> 39. http://lists.ambermd.org/mailman/listinfo/amber
> 40. mailto:AMBER.ambermd.org
> 41. http://lists.ambermd.org/mailman/listinfo/amber
> 42. mailto:AMBER.ambermd.org
> 43. http://lists.ambermd.org/mailman/listinfo/amber
> 44. mailto:AMBER.ambermd.org
> 45. 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
Received on Sat Aug 31 2019 - 03:00:02 PDT
