What are you going to do when you have more than one disulfide bridge?
When you have a multimer? Pdb2pqr obviously "knows" between which pairs
the bonds are so it should be able to give you this information.
If your question is merely about how to split a string or, since you
apparently have a fixed column PDB format, how to extract the mth to
nth charachter, I suggest that you google for it as there are many
possible solution to this. It is not an AMBER related question at
all but one of simple programming.
On Wed, 24 Sep 2014 11:21:40 +0200
James Starlight <jmsstarlight.gmail.com> wrote:
> In my case there are no any marks for the SS bonds in pdb besides 2
> CYX CYX residues because the pdb have been processing using pdb2pqr
> previously to assign all protonation states so the much simple case
> is just to find positions of each CYX residues within the sequence
> using something like grep "ATOM.*\(CYX)" $pdb
> but I have no idea how to obtain the positions of each CYX quickly as
> the individual variable in bash.
>
> 2014-09-24 11:14 GMT+02:00 Hannes Loeffler
> <Hannes.Loeffler.stfc.ac.uk>:
>
> > The formats from the PDB have disulfide bridges marked. If your
> > input file doesn't you could try to do distance-based assignment
> > but this may lead to false negatives and false positives. Another
> > problem is that leap reassigns residue numbers starting with the
> > first it finds and renumbering all subsequent ones by incrementing
> > by one.
> >
> > On Wed, 24 Sep 2014 10:59:04 +0200
> > James Starlight <jmsstarlight.gmail.com> wrote:
> >
> > > Dear Amber users,
> > >
> > >
> > > I wounder about possibilities to define disulphide bond between
> > > any pairs of SG atoms of CYX residues using tleap scripts in some
> > > automatic fashion.
> > >
> > > In my case I use tleap as part of some big script to process many
> > > models for further md simulation. Each of the model consist of
> > > pair of CYX residues (assigned by pdb2pqr) in different positions
> > > of its sequence. So in script I need firstly to know the number
> > > of position for each of CYX residues of each model and than to
> > > fill this numbers to the tleap input files for each model
> > >
> > > in bash for one model it will be look like:
> > >
> > > #some command to scan the sequence of model.pdb and define pair of
> > > its CYX residues within it as the k ans i variables
> > > printf "source leaprc.ff03.r1\nprotein = loadpdb
> > > model.pdb\nsetbox protein centers\nbond protein.${k}.SG
> > > protein.${i}.SG\nsaveamberparm protein protein.parm7
> > > protein.inpcrd\nquit" > ./tleap.in
> > >
> > >
> > > so my task is only to find some command which will scan model and
> > > find positions of the CYX within its sequence which could be put
> > > to the tleap as two digits. It will be better to find those 2
> > > digits using pdb as an input and some unix command like sed or
> > > grep to find positions
> > >
> > > I will be very thankful for any suggestions!
> > >
> > > James
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Received on Wed Sep 24 2014 - 03:00:02 PDT
