Thanks very much to both of you. :) That has resolved the issue.
On Tue, Oct 1, 2013 at 12:54 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Tue, Oct 1, 2013 at 7:48 AM, George Green <soyo.green.gmail.com> wrote:
>
> > Ok, I've finally got a handle on the precise problem I'm having.
> >
> > 1) I have created an input pdb file for leap. It has two protein
> molecules
> > in it that are very similar in structure separated by TER cards. i.e.
> >
> >
> > ########################
> > # Overview of pfb file strucure
> > Residues :1-99
> > TER
> > Residues :1-94
> > TER
> > END
> > ########################
> >
> > So each protein's first residue starts with 1.
> >
> > 2) When opened the pdb in Chimera, the protein appear as intended. i.e.
> as
> > two unconnected, separate entities. So no problems there
> >
> > 3) Each protein contains a disulphide bond that needs to be created in
> > amber. The residue pairs are different residue numbers. As a first
> attempt,
> > which I realized would fail I used the following commands (edited for
> > brevity):
> >
> > source leaprc.gaff
> > source leaprc.ff03.r1
> > mol = loadpdb mou-hum_stage2.pdb
> > # first pdb
> > bond mol.80.SG mol.25.SG
> > #
> > # second pdb
> > bond mol.20.SG mol.75.SG
> > saveamberparm mol test.top test.trj
> >
> > 4) The disulphide bond command fails. So my question is this:
> >
> > *** In this situation, how do I create the disulphide bonds?
> >
>
> You need to use LEaP's numbering, not the numbering in the topology file.
> You can use the "desc" command to see how individual UNITs are arranged in
> tleap. The first residue of the second protein will be residue 100, for
> instance, so the residue indexes of the second disulfide must be
> appropriately adjusted.
>
> It's also always a good idea to visualize the resulting structure from
> tleap to make sure the bonds are what they should be.
>
> HTH,
> Jason
>
>
> >
> > Many thanks.
> >
> >
> >
> >
> >
> >
> > On Mon, Sep 30, 2013 at 4:01 PM, George Green <soyo.green.gmail.com>
> > wrote:
> >
> > > Sorry, here are the further details.
> > >
> > > ###################
> > >
> > > cat<< EOF > PP-inter_step1.lep
> > > source leaprc.gaff
> > > source leaprc.ff03.r1
> > > mou = loadpdb MOUS_XPLORnoH.pdb
> > > hum = loadpdb HUM_XPLORnoH.pdb
> > > savepdb mou mou_stage1.pdb
> > > savepdb hum hum_stage1.pdb
> > > quit
> > > EOF
> > > #
> > > tleap -f PP-inter_step1.lep
> > > #
> > > cat mou_stage1.pdb hum_stage1.pdb > mou-hum_stage2.pdb
> > > grep -v END mou-hum_stage2.pdb > temp
> > > mv -f temp mou-hum_stage2.pdb
> > >
> > > echo ""
> > > echo "step2................."
> > > echo ""
> > >
> > > #
> > > cat<< EOF > PP-inter_step2.lep
> > > source leaprc.gaff
> > > source leaprc.ff03.r1
> > > mol = loadpdb mou-hum_stage2.pdb
> > > savepdb mol test.pdb
> > > saveamberparm mol test.top test.trj
> > > charge mol
> > > quit
> > > EOF
> > > #
> > > tleap -f PP-inter_step2.lep
> > >
> > > ########################
> > >
> > > The two protein are 99 residues each. I ran each through leap, adding
> > > hydrogens, etc and then wrote out a unique pdb file for each. Then I
> used
> > > linux cat to combine the two pdbs into one pdb file; each protein being
> > > separated by a TER card. The final two lines are TER, then END.
> > >
> > > I thought they are treated as the same protein because even though they
> > > are some distance apart, there should be two C-terms and 2-Nterms. one
> > for
> > > each protein. However, leap reported that there is only one of each,
> and
> > > when viewed in chimera, the Nterm of one was connected to the Cterm of
> > the
> > > other by an (unphysical) elongated polypeptide chain.
> > >
> > > However, I seem to have somehow sorted the issue out. Not exactly sure
> > how
> > > and am looking into it now.
> > >
> > > I've used ambpdb to output a pdb of the amber topology files created
> > > (without the initial connected termini issue) and both proteins are
> > > separated by a TER card. However, the residue numbering carries on
> > > sequentially through the file (i.e. :1-198). I had the following
> > questions
> > > that I needed some advice about.
> > >
> > > If there are two proteins in the same amber topology file is there any
> > way
> > > (i.e. some label) to distinguish between the two apart from residue
> > number?
> > >
> > > The situation I have now is that I would have to distinguish between
> > > protein A using residue numbers :1-99, and protein B using residue
> > numbers
> > > :100-198. This is fine in terms of creating the disulphide bonds
> present
> > in
> > > each protein, but will it cause problems down the line in terms of
> > > analysis?
> > >
> > >
> > > Many Thanks
> > >
> > >
> > > On Mon, Sep 30, 2013 at 12:53 PM, David A Case <
> case.biomaps.rutgers.edu
> > >wrote:
> > >
> > >> On Sun, Sep 29, 2013, George Green wrote:
> > >>
> > >> > I have two proteins which I have put into a single pdb file so they
> > are
> > >> > around 10 angstroms apart.
> > >> >
> > >> > However if I separate the two molecules using TER cards they are
> > >> treated as
> > >> > being the same molecule.
> > >>
> > >> We need more information. What made you conclude that the two
> proteins
> > >> were
> > >> being "treated as being the same molecule"? Exactly how did you use
> TER
> > >> cards
> > >> to separate the two molecules? Since we don't know what you did, and
> we
> > >> don't
> > >> know what the error was, people on the list cannot be of much help.
> > >>
> > >> ...dac
> > >>
> > >>
> > >> _______________________________________________
> > >> AMBER mailing list
> > >> AMBER.ambermd.org
> > >> http://lists.ambermd.org/mailman/listinfo/amber
> > >>
> > >
> > >
> >
> >
> > On Tue, Oct 1, 2013 at 12:43 PM, David A Case <case.biomaps.rutgers.edu
> > >wrote:
> >
> > > On Mon, Sep 30, 2013, George Green wrote:
> > >
> > > > cat mou_stage1.pdb hum_stage1.pdb > mou-hum_stage2.pdb
> > > > grep -v END mou-hum_stage2.pdb > temp
> > > > mv -f temp mou-hum_stage2.pdb
> > >
> > > Make sure that the final pdb file actually is correct (i.e. examine it
> > in a
> > > text editor).
> > >
> > > > If there are two proteins in the same amber topology file is there
> any
> > > way
> > > > (i.e. some label) to distinguish between the two apart from residue
> > > number?
> > >
> > > No. The amber atom selections and other analysis tools don't have any
> > > notion
> > > of a chain or stand number. (Our excuse: they were adapted from Midas
> > and
> > > Chimera). I have some thoughts about how we could do this in a
> > reasonably
> > > simple way, but it would still be a fair amount of work.
> > >
> > > ...dac
> > >
> > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Tue Oct 01 2013 - 11:30:13 PDT
