ADL: dont know what this means...???

snoze pa snoze.pa at gmail.com
Fri Mar 28 13:32:58 PDT 2008


Try to build the molecule(receptor) using UCSF chimera. Once the
molecule is ready then you can use it in autodocktools.
goodluck

On Fri, Mar 28, 2008 at 2:06 PM, Garrett M. Morris <garrett at scripps.edu> wrote:
>
>  Dear Namitha,
>
>
>
>  On 28 Mar, 2008, at 4:27 am, namita at ncbs.res.in wrote:
>
>  > Dear users
>  >
>  > Thanks for all the help given so far in helping me solve my issues.
>  > To an
>  > extent I have succeeded in resolving many of my problems but again I
>  > face
>  > many more...pls do help me this time again...
>  >
>  > I try to save in my receptor molecule (which is generated by
>  > modeller) in
>  > pdbqt format. (Grid -> Macromolecule -> Choose)and then saves the
>  > molecule
>  > in pdbqt. when I try opening this molecule again it asks me whether
>  > i need
>  > to preserve charges or add gasteiger charges to it. Either i say no
>  > or yes
>  > to that option it gives me a warning message like this :
>  >
>  > Non-integral charge on molecule:- -6.075
>  >
>  > correct 11 residues:
>  > HIS1 0.055
>  > GLN13 0.006
>  > LYS27 0.006
>  > TYR44 0.03
>  > PRO45 0.03
>  > GLU69 0.029
>  > PRO70 0.03
>  > ARG104 0.029
>  > PRO105 0.03
>  > ASN196 0.006
>  > PRO473 0.058
>  > Charges should be corrected in written output file!
>  >
>  > I would like to know how and where do i need to add these charges? Are
>  > they talking about the .pdbqt output file??
>
>  Yes.
>
>
>  >
>  >
>  > Please help...any help would be greatly appreciated.
>
>  Sorry if this message from ADT is not clear.
>
>  One check ADT does on the macromolecule is to add up all the partial
>  charges on each residue, to see if they sum to an integer.  The idea
>  is that a side chain can be neutral or charged, but never carry a
>  fractional electron...  This kind of error check can detect when there
>  are missing atoms in a sidechain, something that is important in
>  guaranteeing your molecular model is accurate.
>
>  These discrepancies are very small for each amino acid, so I would not
>  worry about them too much.  I will talk with the ADT programmers about
>  this.  You can actually edit the charges in the PDBQT file using a
>  text editor.
>
>  Thanks,
>
>  Garrett
>
>
>  >
>  >
>  > Thanks
>  > Namitha
>  >
>  > ________________________________________________
>  > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
>  > ---
>
>  ___
>  Dr Garrett M. Morris, MA (Oxon), DPhil (Oxon)
>
>  The Scripps Research Institute,       tel: (858) 784-2292
>  Dept. Molecular Biology,  MB-5,       fax: (858) 784-2860
>  10550  North Torrey Pines Road,       email: garrett at scripps.edu
>  La Jolla,  CA 92037-1000,  USA.       mgl.scripps.edu/people/gmm
>
>
>
>
>
>
>
>  ________________________________________________
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>


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