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
> >
> >
> > _______________________________________________
> > 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
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Oct 01 2013 - 05:00:16 PDT
