ADL: strange error in autodock4 output

snoze pa snoze.pa at gmail.com
Mon Mar 3 10:26:27 PST 2008


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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