Re: [AMBER] bash scripting for MD tasks

From: Hannes Loeffler <>
Date: Wed, 24 Sep 2014 10:14:55 +0100

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 <> 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" > ./
> 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 - 02:30:02 PDT
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