Thanks Jerome, that was the issue, problem solved!
It's the first time I deal with NAs and I should have certainly read more
carefully AT12 manual..!
Best,
On 7 February 2013 14:00, <Jerome.GOLEBIOWSKI.unice.fr> wrote:
> 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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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> -------------------------
> 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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--
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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Received on Thu Feb 07 2013 - 07:00:03 PST
