Re: [AMBER] Generating topology files for two proteins in a single input pdb

From: George Green <>
Date: Mon, 30 Sep 2013 16:01:04 +0100

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
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.trj
charge mol
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

Many Thanks

On Mon, Sep 30, 2013 at 12:53 PM, David A Case <>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
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Received on Mon Sep 30 2013 - 08:30:12 PDT
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