ADL: strange error in autodock4 output

snoze pa snoze.pa at gmail.com
Mon Mar 3 13:04:50 PST 2008


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    -0.084Cl

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     0.210HD


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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