Hi max,
it seems that your NA structure is not caped properly,
you have phosphate atoms in the 5' ends of your double helixin the XRay
structure.
It's not supposed to be the caseif it is a "real" 5'.
Check the structure of a DG5 alone in xleap.
This was probably not the case in your previous structure.
Best,
Jerome
On 02/07/2013 12:45 PM, Massimiliano Porrini wrote:
> 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,
>
>
>
>
>
>
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--
-------------------------
Jérôme Golebiowski
Institute of Chemistry - NICE, UMR 7272
Molecular Modeling team
University of Nice Sophia Antipolis, Parc Valrose
06108 Nice cedex 2. FRANCE
http://www.unice.fr/icn/golebiowski
Centre Documentaire Informatique pour l'Enseignement de la Chimie : CDIEC.
Département de Chimie
?Université de Nice Sophia Antipolis, Parc Valrose
06108 Nice cedex 2
http://www.unice.fr/cdiec
tel +33 (0)4 92 07 61 20
fax +33 (0)4 92 07 61 25
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Received on Thu Feb 07 2013 - 05:30:03 PST
