[rDock-list-def] Numerous warnings about undefined Tripos types for protein atoms

[Hassan G. <hg...@us...>]

Hi,

I'm using rDock version '2013.1' which I just downloaded and built from
source on Ubuntu 14.

When I run both rbcavity and rbdock I get numerous warnings of the
following sort:

RbtMOL2FileSource: WARNING Undefined Tripos type for UNK:-_0.3716:NH1
RbtMOL2FileSource: WARNING Undefined Tripos type for UNK:-_0.3716:NH2
RbtMOL2FileSource: WARNING Undefined Tripos type for UNK:-_0.2463:OD1
RbtMOL2FileSource: WARNING Undefined Tripos type for UNK:-_0.2463:OD2

I believe my receptor mol2 file has Tripos atom types in it. Here are a few
lines from the receptor mol2 file:


   2235  CB         1.4470  -16.9190   28.2910 C.3   177  ASP177      0.0760
   2236  CG         1.9440  -18.2290   28.8890 C.2   177  ASP177      0.3582
   2237  OD1        2.4870  -19.0550   28.1260 O.co2 177  ASP177     -0.2463
   2238  OD2        1.7740  -18.4410   30.1130 O.co2 177  ASP177     -0.2463
   2239  H01        0.9500  -17.1340   27.3450 H     177  ASP177      0.0402

I prepared this receptor file by using OpenBabel to convert the PDB to
mol2. The Tripos atom types are in the column immediately after the
coordinates. Is this not the correct place for the Tripos atom types to be
listed?

Thank you for your help. And as always, thank for your maintenance of a
great open source docking program.

Sincerely,
Hassan Ghani, MD