On 16/08/17 22:09, Geoffrey Hutchison wrote:
obabel -ipdb 3nya.pdb -opdbqt -xrp > 3nya.pdbqt
According to the manual:
r Output as a rigid molecule (i.e. no branches or torsion tree)
removing the option does put the side chains back, but makes them
flexible instead (creates active torsi
Hi David,
I just noticed this question, I've missed it too.
I've tried with your test and I've noticed that the residue is in fact there, but some
renumbering occurs (no idea why):
$ obabel -ipdb 3nya.pdb -opdbqt -xrp > 3nya.pdbqt
1 molecule converted
$ grep "TRP A 1" 3nya.pdbqt
ATOM 1
Sorry - I saw that no one responded. I haven't used the PBQT format myself, but:
r Output as a rigid molecule (i.e. no branches or torsion tree)
So my guess is that the -xr is removing the side chain perhaps?
-Geoff
> On Aug 2, 2017, at 4:14 AM, David van der Spoel wrote:
>
> Hi,
>
> I
Hi,
I am trying to generate pdbqt input for Autodock and friends using
obabel -ipdb 3nya.pdb -opdbqt -xrp > 3nya.pdbqt
Input for first residue:
ATOM 1 N TRP A 32 -17.931 26.881 -57.510 1.00 84.68
N
ATOM 2 CA TRP A 32 -18.091 25.544 -56.851 1.00 84.93
C
AT