ADL: strange error in autodock4 output

snoze pa snoze.pa at gmail.com
Wed Mar 12 14:08:55 PDT 2008


Any help from the auto dock developers in this issue.
thanks in advance

On Mon, Mar 3, 2008 at 4:04 PM, snoze pa <snoze.pa at gmail.com> wrote:

> Dear  Ruth and autodock users,
>
> I am getting some unexpected format problem while dealing with number of
> ligand files having Cl atom. Can you check this format in file constants.h,
> specially the line FORMAT_PDBQT_ATOM_RESSTR
>
> in my ligand f PDBQT file i have a line
>
> ATOM     12 Cl           0      -4.035   1.155  -0.356  0.00  0.00    -
> 0.084 Cl
>
> while i am getting the following line in my dlg file. This seems to be
> unexpected as 'Cl' atom is replaced by 'l' while printing in dlg file.
>
> ATOM     12  l           0     -27.578  98.592  16.732 -0.55 -0.02    -
> 0.084 98.511
>
> Which is trivial because the way dlg file is written based on following
> format of pdbqt file
>
> ATOM     10  HO4 PGP     1      22.065  29.222  38.002  1.00  0.00
> 0.210 HD
>
>
> We have two spaces after the atom number(10 and HO4) in autodock4 format(
> constants.h file) while the pdbqt file i am using have only one space
> between atom number and atom name. During the PDBQT reading it is working
> fine as i can see from dlg file that all records are printed properly. While
> in writing dlg file  it is printing based on following format and missing C
> from Cl(because we have two spaces between %5d  %.13s).
>
> #define FORMAT_PDBQ_ATOM_RESSTR         "%sATOM  %5d  %.13s
> %8.3f%8.3f%8.3f%+6.2f%+6.2f    %+6.3f"
>
> What do you think?
>
> Thanks for your help
>
> s
>
> >
> >
> >
> > On Mon, Mar 3, 2008 at 12:26 PM, snoze pa <snoze.pa at gmail.com> wrote:
> >
> > > In my case i figure out the probelm. I think the error was related to
> > > how prepare_ligand4.py make ligand.pdbqt file
> > >
> > > it the input file format for atom entry is following then it is
> > > printing 'l' instead of 'Cl'
> > >
> > > check Cl position, C is left
> > >
> > > ATOM     15  O           0      -0.110  -1.804   0.096  0.00  0.00
> > > ATOM     16 Cl           0      -3.935   2.652   0.047  0.00  0.00
> > > ATOM     17 Cl           0      -2.939  -2.655   0.110  0.00  0.00
> > > ATOM     18  N           0       1.770  -0.158   0.078  0.00  0.00
> > >
> > >
> > > if the atom format is following in ligand.pdbqt file then it  is
> > > printing correct atom name for
> > > 'Cl'.  Check Cl is moved toward the right.
> > >
> > > ATOM     15  O           0      -0.110  -1.804   0.096  0.00  0.00
> > > ATOM     16  Cl          0      -3.935   2.652   0.047  0.00  0.00
> > > ATOM     17  Cl          0      -2.939  -2.655   0.110  0.00  0.00
> > > ATOM     18  N           0       1.770  -0.158   0.078  0.00  0.00
> > >
> > > If anyone is getting this kind of atom name in dlg file then above may
> > > be helpful. This solved my problem.
> > > s
> > >
> > >
> > >
> > > On Mon, Mar 3, 2008 at 11:50 AM, snoze pa <snoze.pa at gmail.com> wrote:
> > >
> > > > Dear Autodock users,
> > > >  I am not sure if you are also getting incorrect atom name for 'Cl'
> > > > in your dlg files but I am getting atom name 'l' instead of 'Cl'.  I have
> > > > some 100 different ligand that have 'Cl' atom but the autodock4(pre
> > > > compiled) version is printing only 'l' not 'Cl' in the dlg files. I will
> > > > highly appreciate anyy help in this matter.
> > > > thanks in advance
> > > > s
> > > >
> > > >
> > > >
> > >
> >
>


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