Glad you figured it out!
I'm guessing you didn't put a TER card between those two residues? They
aren't in canonical tleap order, so it might be by accident that the bonding
happened properly. This just FYI in case a similar case doesn't work in the
future. The leaps do pretty well with guesses at bonding, but sugars can be
complicated, so they sometimes need a little help.
On Mon, Aug 15, 2011 at 2:32 PM, Yun Shi <yunshi09.gmail.com> wrote:
> Sorry, when I checked
>
> desc 1m7.441.O
> ATOM
> Name: O
> Type: OS
> Charge: -0.4580
> Polarization: 0.0000
> Element: O
> Atom flags: (decimal 131072 hex 0x20000)
> posfxd n posblt n posdrwn n selected n
> pert n notdisp n touched n posknwn Y
> internal n needsmin n needsbuild n
> Atom position: -5.752000, 12.674000, 33.641000
> Atom velocity: 0.000000, 0.000000, 0.000000
> Bonded to .R<OME 441>.A<CH3 2> by a single bond.
> Bonded to .R<2hA 440>.A<C1 1> by a single bond.
>
> So without my using bond command, the bonds are already there, and I do see
> those bonds in VMD.
>
> Sorry for the false alarm[?][?]
>
> On Mon, Aug 15, 2011 at 11:10 AM, Yun Shi <yunshi09.gmail.com> wrote:
>
> > Hi,
> >
> > There seems to be some small problems still.
> >
> > So I load ff99SB and GLYCAM_06 with source command, them load my pdb file
> > as
> >
> > > 1m7 = loadpdb 1m7iF.pdb
> >
> > Loading PDB file: ./1m7iF.pdb
> > total atoms in file: 3379
> > Leap added 3284 missing atoms according to residue templates:
> > 3284 H / lone pairs
> > > bond 1m7.441.O 1m7.440.C1
> > > saveamberparm 1m7 1m7iff.prmtop 1m7iff.inpcrd
> > Checking Unit.
> > WARNING: The unperturbed charge of the unit: 1.000000 is not zero.
> >
> > -- ignoring the warning.
> >
> > Building topology.
> > Building atom parameters.
> > Building bond parameters.
> > Building angle parameters.
> > Building proper torsion parameters.
> > !FATAL ERROR----------------------------------------
> > !FATAL: In file [unitio.c], line 1773
> > !FATAL: Message: 1-4: cannot add bond 6639 6663
> > This may be caused by duplicate bond specifications;
> > for example, explicit bond commands in addition to PDB conect records.
> > !
> > !ABORTING.
> >
> > But then I checked the the resulting pdb file from "savepdb 1m7
> > 1m7iff.pdb", which showed that there are empty valence for atoms 6639
> > (1m7.440.C1) and 6663 (1m7.441.O ), so could you let me know why the
> single
> > bond (by default) cannot be added?
> >
> > Thanks,
> >
> > Yun
> >
> >
> >
> >
> > On Sat, Aug 13, 2011 at 11:39 AM, Lachele Foley (Lists) <
> lf.list.gmail.com
> > > wrote:
> >
> >> It means the files are ok for a normal MD simulation.
> >>
> >> Of course, as always, I do recommend opening the prmtop and inpcrd
> >> files in VMD (VMD file types AMBER7 Parm and AMBER7 Restart,
> >> respectively). Carefully inspect to be sure bonding looks ok, etc.
> >>
> >> It is also useful to try the "check" command in tleap. It doesn't
> >> catch everything, but can alert you to long bonds and such. To do
> >> that, just before the saveamberparm bit, enter "check 1M7".
> >>
> >> :-) L
> >>
> >> On Sat, Aug 13, 2011 at 1:09 PM, Yun Shi <yunshi09.gmail.com> wrote:
> >> > Thank you! That's really helpful.
> >> >
> >> > But when I tried saving the parameters .prmtop file and .inpcrd file,
> >> > problems appeared as
> >> >
> >> > ...
> >> >
> >> > Marking per-residue atom chain types.
> >> > (Residues lacking connect0/connect1 -
> >> > these don't have chain types marked:
> >> >
> >> > res total affected
> >> >
> >> > CARG 1
> >> > CPRO 1
> >> > NASP 1
> >> > NGLU 1
> >> > WAT 15773
> >> > )
> >> > (no restraints)
> >> >
> >> > So I do not quite understand what "don't have chain types marked:"
> >> means.
> >> > And they are all terminal AAs and waters. I searched the archive and
> >> someone
> >> > said:
> >> >
> >> > If connect0/connect1 are not specified, you just get the warning,
> >> > which has no effect unless you use carnal or the chain part of the
> >> > GROUP spec in sander etc.
> >> >
> >> > So does this mean they won't affect a normal MD simulation?
> >> >
> >> > Thanks,
> >> >
> >> > Yun
> >> >
> >> > On Sat, Aug 13, 2011 at 7:54 AM, Lachele Foley (Lists) <
> >> lf.list.gmail.com>wrote:
> >> >
> >> >> The protein should contain hydrogens. You need to load a protein
> >> >> force field as well as the Glycam force field. The latter only
> >> >> contains protein information as is required for linking glycans to
> >> >> proteins.
> >> >>
> >> >> Try adding "source leaprc.ff99SB" to your leap input file. Put it
> >> >> before the source of leaprc.GLYCAM_06. There are other protein force
> >> >> fields, but that one works.
> >> >>
> >> >> Since you are using amber11+, make sure you build using tleap and not
> >> >> sleap.
> >> >>
> >> >>
> >> >>
> >> >> On Sat, Aug 13, 2011 at 12:26 AM, Yun Shi <yunshi09.gmail.com>
> wrote:
> >> >> > So it's like:
> >> >> >
> >> >> > Welcome to LEaP!
> >> >> > (no leaprc in search path)
> >> >> >> source leaprc.GLYCAM_06
> >> >> > ----- Source: /usr/local/amber11-12/dat/leap/cmd/leaprc.GLYCAM_06
> >> >> > ----- Source of /usr/local/amber11-12/dat/leap/cmd/leaprc.GLYCAM_06
> >> done
> >> >> > Loading parameters:
> >> /usr/local/amber11-12/dat/leap/parm/Glycam_06g.dat
> >> >> > Reading title:
> >> >> > GLYCAM PARAMETERS (FOR AMBER 8.0, RESP 0.010), COPYRIGHT CCRC 2004
> >> >> > Loading Prep file:
> /usr/local/amber11-12/dat/leap/prep/GLYCAM_06.prep
> >> >> > Loading library:
> >> /usr/local/amber11-12/dat/leap/lib/GLYCAM_amino_06.lib
> >> >> > Loading library:
> >> /usr/local/amber11-12/dat/leap/lib/GLYCAM_aminoct_06.lib
> >> >> > Loading library:
> >> /usr/local/amber11-12/dat/leap/lib/GLYCAM_aminont_06.lib
> >> >> > Loading library: /usr/local/amber11-12/dat/leap/lib/solvents.lib
> >> >> >> 1M7 = loadpdb 1m7iF.pdb
> >> >> > Loading PDB file: ./1m7iF.pdb
> >> >> > Unknown residue: ASP number: 0 type: Terminal/beginning
> >> >> > ..relaxing end constraints to try for a dbase match
> >> >> > -no luck
> >> >> > Unknown residue: VAL number: 1 type: Nonterminal
> >> >> > ...
> >> >> >
> >> >> > I am doing this on a cluster, which allegedly contains all the
> >> things. So
> >> >> no
> >> >> > hydrogen atoms for amino acids is normal?
> >> >> >
> >> >> > Thanks again!
> >> >> >
> >> >> > Yun
> >> >> >
> >> >> > On Fri, Aug 12, 2011 at 7:27 PM, Lachele Foley (Lists) <
> >> >> lf.list.gmail.com>wrote:
> >> >> >
> >> >> >> How did you load your protein force field? Did you use one of the
> >> >> >> standard leaprc's down in $AMBERHOME/dat/leap/cmd?
> >> >> >>
> >> >> >> My best guess is that you didn't load library files for N- and
> >> >> >> C-terminal amino acids. For example, to load the params for ff94,
> >> you
> >> >> >> need all three of: all_amino94.lib, all_aminoct94.lib &
> >> >> >> all_aminont94.lib. The "ct" and "nt" versions contain the
> terminal
> >> >> >> groups.
> >> >> >>
> >> >> >> The leaprc's that ship with Amber generally load all these. So,
> if
> >> >> >> you're making a custom one, you might try looking in, say,
> >> >> >> leaprc.ff99SB, to see what all is frequently needed.
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> On Fri, Aug 12, 2011 at 10:11 PM, Yun Shi <yunshi09.gmail.com>
> >> wrote:
> >> >> >> > Thanks Lachele!
> >> >> >> >
> >> >> >> > I initially thought TER card would take up one atom numbering,
> but
> >> it
> >> >> >> turned
> >> >> >> > out not, meaning I do not have to renumbering subsequent atoms
> >> every
> >> >> time
> >> >> >> I
> >> >> >> > add a TER card.
> >> >> >> >
> >> >> >> > So my oligosaccharide seems to be recognized by GLYCAM_06 ff.
> >> >> >> >
> >> >> >> > But when I loaded the protein-sugar complex into tleap with
> >> GLYCAM_06
> >> >> ff,
> >> >> >> it
> >> >> >> > seems those terminal amino acids were not recognized. I got
> screen
> >> >> info
> >> >> >> such
> >> >> >> > as:
> >> >> >> >
> >> >> >> > Unknown residue: ASP number: 0 type: Terminal/beginning
> >> >> >> > ..relaxing end constraints to try for a dbase match
> >> >> >> > -no luck
> >> >> >> > ...
> >> >> >> > Unknown residue: PRO number: 434 type: Terminal/last
> >> >> >> > ..relaxing end constraints to try for a dbase match
> >> >> >> > -no luck
> >> >> >> > ...
> >> >> >> >
> >> >> >> > But every amino acid residue (including terminal ones) had its
> new
> >> >> >> residue
> >> >> >> > created, like
> >> >> >> >
> >> >> >> > ...
> >> >> >> > Creating new UNIT for residue: PRO sequence: 435
> >> >> >> > Created a new atom named: N within residue: .R<PRO 435>
> >> >> >> > Created a new atom named: CA within residue: .R<PRO 435>
> >> >> >> > Created a new atom named: C within residue: .R<PRO 435>
> >> >> >> > Created a new atom named: O within residue: .R<PRO 435>
> >> >> >> > Created a new atom named: CB within residue: .R<PRO 435>
> >> >> >> > Created a new atom named: CG within residue: .R<PRO 435>
> >> >> >> > Created a new atom named: CD within residue: .R<PRO 435>
> >> >> >> > Created a new atom named: OXT within residue: .R<PRO 435>
> >> >> >> > ...
> >> >> >> >
> >> >> >> > So why there is no hydrogen atoms? Do I need to manually add
> them?
> >> I
> >> >> >> asked
> >> >> >> > this because hydrogen atoms on my oligosaccharide were added
> >> >> >> automatically
> >> >> >> > with loadpdb command, as
> >> >> >> > Leap added 57 missing atoms according to residue templates:
> >> >> >> > 57 H / lone pairs
> >> >> >> > The file contained 3323 atoms not in residue templates
> >> >> >> >
> >> >> >> > And the total charge is 0 now, which should be +1 according to
> the
> >> >> >> protein's
> >> >> >> > COO and NH3 sidechains (the sugar is neutral).
> >> >> >> >
> >> >> >> > Could anyone please help me out?
> >> >> >> >
> >> >> >> > Thank you.
> >> >> >> >
> >> >> >> > Yun
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> > On Fri, Aug 12, 2011 at 11:28 AM, Lachele Foley (Lists)
> >> >> >> > <lf.list.gmail.com>wrote:
> >> >> >> >
> >> >> >> >> Before reordering, I would just insert TER cards between each
> >> >> residue.
> >> >> >> >> This will instruct leap not to try bonding them. Then, in
> leap,
> >> you
> >> >> >> >> can use the "bond" command to link the residues together
> >> properly.
> >> >> >> >> Still laborious, but not quite as much.
> >> >> >> >>
> >> >> >> >> Sorry... no script.
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> On Fri, Aug 12, 2011 at 1:53 PM, Yun Shi <yunshi09.gmail.com>
> >> wrote:
> >> >> >> >> > Thanks a lot Lachele!
> >> >> >> >> >
> >> >> >> >> > You are right that the ordering of my molecule is reverse.
> But
> >> >> >> changing
> >> >> >> >> the
> >> >> >> >> > ordering manually seems to be laborious, do you have a script
> >> to do
> >> >> >> this
> >> >> >> >> > kind of thing as there are also CONECT records in the pdb
> file?
> >> >> >> >> >
> >> >> >> >> > Anyways, I will try changing the order manually first.
> >> >> >> >> >
> >> >> >> >> > Yun
> >> >> >> >> >
> >> >> >> >> > On Fri, Aug 12, 2011 at 10:29 AM, Lachele Foley (Lists)
> >> >> >> >> > <lf.list.gmail.com>wrote:
> >> >> >> >> >
> >> >> >> >> >> The ordering of the atoms shouldn't matter. The ordering
> of
> >> the
> >> >> >> >> >> residues can make a huge difference.
> >> >> >> >> >>
> >> >> >> >> >> For example, if you have DGlcpa1-4DManpA1-OH, the three
> >> residues
> >> >> are,
> >> >> >> >> >> in the order of that string, "0GA", "4MA" and "ROH".
> However,
> >> in
> >> >> the
> >> >> >> >> >> pdb file, they need to be ordered ROH first, then 4MA and
> 0GA.
> >> >> >> >> >>
> >> >> >> >> >> If the ordering is wrong, you can get around it by inserting
> >> TER
> >> >> >> cards
> >> >> >> >> >> between all the residues and setting the bonding explicitly
> in
> >> >> tleap.
> >> >> >> >> >>
> >> >> >> >> >> If that still doesn't help, send me your pdb file (you don't
> >> have
> >> >> to
> >> >> >> >> >> send to the list), and I'll help.
> >> >> >> >> >>
> >> >> >> >> >> :-) Lachele
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >> On Fri, Aug 12, 2011 at 1:19 PM, Yun Shi <
> yunshi09.gmail.com>
> >> >> wrote:
> >> >> >> >> >> > Thank you for the reply.
> >> >> >> >> >> >
> >> >> >> >> >> > But I want to keep the coordinates as in the original pdb
> >> file,
> >> >> and
> >> >> >> I
> >> >> >> >> do
> >> >> >> >> >> > notice that the ordering of atoms in my pdb file are
> >> different
> >> >> from
> >> >> >> >> >> GLYCAM
> >> >> >> >> >> > convention.
> >> >> >> >> >> >
> >> >> >> >> >> > So could anyone suggest a way to format my oligosaccharide
> >> in
> >> >> >> >> accordance
> >> >> >> >> >> > with GLYCAM06 while retaining the coordinates (structure)
> of
> >> my
> >> >> >> >> original
> >> >> >> >> >> pdb
> >> >> >> >> >> > file?
> >> >> >> >> >> >
> >> >> >> >> >> > Thanks,
> >> >> >> >> >> >
> >> >> >> >> >> > Yun
> >> >> >> >> >> >
> >> >> >> >> >> >
> >> >> >> >> >> > On Fri, Aug 12, 2011 at 10:00 AM, Oliver Grant <
> >> >> >> >> olivercgrant.gmail.com
> >> >> >> >> >> >wrote:
> >> >> >> >> >> >
> >> >> >> >> >> >> Hi,
> >> >> >> >> >> >>
> >> >> >> >> >> >> Not sure what the problem is without looking at your pdb
> >> input
> >> >> >> file.
> >> >> >> >> I
> >> >> >> >> >> >> suggest going to glycamweb and building your
> >> oligosaccharide
> >> >> and
> >> >> >> >> >> comparing
> >> >> >> >> >> >> that to what you have.
> >> >> >> >> >> >>
> >> >> >> >> >> >> Oliver
> >> >> >> >> >> >>
> >> >> >> >> >> >> On 12 August 2011 04:42, Yun Shi <yunshi09.gmail.com>
> >> wrote:
> >> >> >> >> >> >>
> >> >> >> >> >> >> > Hi All,
> >> >> >> >> >> >> >
> >> >> >> >> >> >> > Sorry for this lower-level question, but I searched the
> >> >> archive
> >> >> >> and
> >> >> >> >> >> still
> >> >> >> >> >> >> > did not solve it.
> >> >> >> >> >> >> >
> >> >> >> >> >> >> > So I was trying to load a pdb file (only one
> >> oligosaccharide
> >> >> >> >> molecule)
> >> >> >> >> >> >> > after
> >> >> >> >> >> >> > source leaprc.GLYCAM_06, but what I got was
> >> >> >> >> >> >> >
> >> >> >> >> >> >> > ERROR: Comparing atoms
> >> >> >> >> >> >> > .R<0hA 1>.A<C3 14>,
> >> >> >> >> >> >> > .R<0hA 1>.A<C1 1>,
> >> >> >> >> >> >> > .R<0hA 1>.A<H2 19>, and
> >> >> >> >> >> >> > .R<0hA 1>.A<O2 20>
> >> >> >> >> >> >> > to atoms
> >> >> >> >> >> >> > .R<0hA 1>.A<C3 14>,
> >> >> >> >> >> >> > .R<2hA 1>.A<C1 1>,
> >> >> >> >> >> >> > .R<0hA 1>.A<H2 19>, and
> >> >> >> >> >> >> > .R<0hA 1>.A<C1 1>
> >> >> >> >> >> >> > This error may be due to faulty Connection atoms.
> >> >> >> >> >> >> > !FATAL ERROR----------------------------------------
> >> >> >> >> >> >> > !FATAL: In file [chirality.c], line 140
> >> >> >> >> >> >> > !FATAL: Message: Atom named C1 from 2hA did not
> match
> >> !
> >> >> >> >> >> >> > !
> >> >> >> >> >> >> > !ABORTING.
> >> >> >> >> >> >> >
> >> >> >> >> >> >> > So what it really means by "faulty Connection atoms"? I
> >> have
> >> >> >> >> already
> >> >> >> >> >> >> > changed
> >> >> >> >> >> >> > the sugar names according to GLYCAM naming convention.
> >> >> >> >> >> >> >
> >> >> >> >> >> >> > Any help is appreciated!
> >> >> >> >> >> >> >
> >> >> >> >> >> >> > Yun
> >> >> >> >> >> >> > _______________________________________________
> >> >> >> >> >> >> > 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
> >> >> >> >> >> >>
> >> >> >> >> >> > _______________________________________________
> >> >> >> >> >> > 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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 15 2011 - 12:00:05 PDT
