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
>
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Received on Fri Aug 12 2011 - 21:30:03 PDT
