Dear Amber users,
I am trying to create topology and coordinates files with tleap
from the X-ray PDB file of a protein dimer bound to DNA, but I am getting
some errors.
I enclose the PDB file revised by me:
- I deleted crystallization water molecules and two organic molecules;
- I renamed few HIS to HIE, CYS to CYM (they coordinate zinc ions);
- I renamed the two zinc-containing residues to ZNA and ZNB (I am just
considering
the zinc dications tetra-coordinated in a non-bonded model);
- I added two TER cards where some residues are missing because they were
not located in the experiment (this action is just to have preliminary
Amber input files,
the idea is to add at some point the missing residues with modelling
techniques).
Here is the tleap input file I am using:
source leaprc.ff99SBildn
set default PBradii mbondi2
pdna = loadPdb file_rev.pdb
set pdna.ZNA.ZN type Zn
set pdna.ZNA.ZN charge 2.0000
set pdna.ZNB.ZN type Zn
set pdna.ZNB.ZN charge 2.0000
saveAmberParm pdna pdna.parm7 pdna.crd
quit
And enclosed there are the leap.log and the error messages (tleap.out)
printed by tleap to the
standard output.
I could not figure out what's wrong with my procedure, as it worked perfectly
with a similar system (a protein tetramer bound to DNA).
Any hint on what's happening here would be very appreciated.
All the best,
--
Dr Massimiliano Porrini
Institut Européen de Chimie et Biologie (IECB)
CNRS UMR 5248 Chimie et Biologie des Membranes et des Nano-objets (CBMN)
2, rue Robert Escarpit
33607 Pessac Cedex
FRANCE
Tel : 33 (0)5 40 00 30 31
Fax : 33 (0)5 40 00 22 00
http://www.iecb.u-bordeaux.fr/
Emails: m.porrini.iecb.u-bordeaux.fr
M.Porrini.ed.ac.uk
maxp.iesl.forth.gr
mozz76.gmail.com
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- application/octet-stream attachment: leap.log
- application/octet-stream attachment: tleap.out
Received on Thu Feb 07 2013 - 04:00:03 PST
