Re: [Open Babel] Pdbqt output missing protein side chains

2017-08-16 Thread David van der Spoel
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

Re: [Open Babel] Pdbqt output missing protein side chains

2017-08-16 Thread Stefano Forli
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

Re: [Open Babel] Pdbqt output missing protein side chains

2017-08-16 Thread Geoffrey Hutchison
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

[Open Babel] Pdbqt output missing protein side chains

2017-08-02 Thread David van der Spoel
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