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
>
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Received on Mon Aug 15 2011 - 11:30:43 PDT
