Date: Mon, 15 Aug 2011 11:32:09 -0700
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
>>
>
>
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