On Fri, Sep 18, 2015 at 2:21 AM, Atila Petrosian <atila.petrosian.gmail.com>
wrote:
> Dear David,
>
> > If you just name your ligand "LIG", reduce won't be able to help. If
> this
> > really came from a pdb entry, us the residue name in the PDB entry: that
> is
> > what reduce knows about.
>
> My ligand is new and it does not coe from a pdb entry.
> I did docking to get protein-ligand complex.
>
> > ??? Looks like you gave it a pdb file with more than just the ligand(?).
> > I don't see any warnings like this when I run reduce on your "lig.pdb"
> file.
>
> What is your mean?
>
>
> ----------------------------------------------------------------------------------------------
> I add H atoms using h_add in pymol (lig_h.pdb).
>
> HETATM 1 N LIG A1100 25.838 24.320 115.794 1.00 0.00
> N
> HETATM 2 N LIG A1100 30.038 19.216 116.208 1.00 0.00
> N
> HETATM 3 N LIG A1100 30.295 17.907 115.854 1.00 0.00
> N
> HETATM 4 C LIG A1100 28.099 20.746 115.724 1.00 0.00
> C
> HETATM 5 C LIG A1100 26.984 20.842 116.556 1.00 0.00
> C
> HETATM 6 C LIG A1100 26.240 22.020 116.605 1.00 0.00
> C
> HETATM 7 C LIG A1100 26.580 23.117 115.812 1.00 0.00
> C
> HETATM 8 C LIG A1100 27.705 23.031 114.984 1.00 0.00
> C
> HETATM 9 C LIG A1100 28.459 21.851 114.942 1.00 0.00
> C
> HETATM 10 C LIG A1100 24.486 24.441 115.547 1.00 0.00
> C
> HETATM 11 C LIG A1100 23.883 25.803 115.499 1.00 0.00
> C
> HETATM 12 C LIG A1100 23.451 26.189 114.208 1.00 0.00
> C
> HETATM 13 C LIG A1100 22.787 27.392 113.983 1.00 0.00
> C
> HETATM 14 C LIG A1100 22.536 28.241 115.050 1.00 0.00
> C
> HETATM 15 C LIG A1100 22.952 27.883 116.333 1.00 0.00
> C
> HETATM 16 C LIG A1100 23.625 26.667 116.574 1.00 0.00
> C
> HETATM 17 C LIG A1100 24.040 26.405 117.972 1.00 0.00
> C
> HETATM 18 C LIG A1100 28.857 19.512 115.701 1.00 0.00
> C
> HETATM 19 C LIG A1100 29.276 17.519 115.116 1.00 0.00
> C
> HETATM 20 C LIG A1100 29.011 16.262 114.443 1.00 0.00
> C
> HETATM 21 C LIG A1100 27.883 16.110 113.623 1.00 0.00
> C
> HETATM 22 C LIG A1100 27.632 14.904 112.978 1.00 0.00
> C
> HETATM 23 C LIG A1100 28.501 13.829 113.148 1.00 0.00
> C
> HETATM 24 C LIG A1100 29.629 13.967 113.963 1.00 0.00
> C
> HETATM 25 C LIG A1100 29.887 15.180 114.602 1.00 0.00
> C
> HETATM 26 O LIG A1100 23.724 23.508 115.301 1.00 0.00
> O
> HETATM 27 O LIG A1100 24.654 25.435 118.372 1.00 0.00
> O
> HETATM 28 O LIG A1100 23.731 27.425 118.794 1.00 0.00
> O
> HETATM 29 O LIG A1100 28.313 18.482 114.991 1.00 0.00
> O
> HETATM 30 H LIG A1100 26.367 25.163 116.008 1.00 0.00
> H
> HETATM 31 H LIG A1100 23.257 28.075 118.235 1.00 0.00
> H
> HETATM 32 H01 LIG A1100 30.773 15.286 115.227 1.00 0.00
> H
> HETATM 33 H02 LIG A1100 26.692 19.991 117.172 1.00 0.00
> H
> HETATM 34 H03 LIG A1100 25.381 22.085 117.272 1.00 0.00
> H
> HETATM 35 H04 LIG A1100 27.995 23.884 114.370 1.00 0.00
> H
> HETATM 36 H05 LIG A1100 29.334 21.792 114.295 1.00 0.00
> H
> HETATM 37 H06 LIG A1100 23.644 25.525 113.365 1.00 0.00
> H
> HETATM 38 H07 LIG A1100 22.467 27.664 112.977 1.00 0.00
> H
> HETATM 39 H08 LIG A1100 22.016 29.185 114.887 1.00 0.00
> H
> HETATM 40 H09 LIG A1100 22.753 28.557 117.166 1.00 0.00
> H
> HETATM 41 H10 LIG A1100 27.196 16.946 113.490 1.00 0.00
> H
> HETATM 42 H11 LIG A1100 26.755 14.800 112.339 1.00 0.00
> H
> HETATM 43 H12 LIG A1100 28.302 12.882 112.647 1.00 0.00
> H
> HETATM 44 H13 LIG A1100 30.308 13.125 114.099 1.00 0.00
> H
>
Now all of your carbon, nitrogen, and oxygen atoms have exactly the same
name. tleap works by matching atom names within residue templates with the
residues in units, adding the atoms that were not defined (and emitting
warnings about atoms that are in the PDB, but not in the residue template
-- these result in fatal errors when trying to save a prmtop).
One of the limitations in this approach is that all atoms *must* have
unique names in a residue, which is clearly not the case here. antechamber
may have made all of the atoms unique (by appending a number to the name)
-- I'm not sure; you would have to check the mol2 file for that. But
regardless, it certainly won't work for the PDB file you seem to be using
here.
> END
>
> ----------------------------------------------------------------------------------------------------
>
> When I used following for only ligand:
>
> $AMBERHOME/exe/antechamber -i lig_h.pdb -fi pdb -o lig_h.mol2 -fo mol2 -c
> bcc -s 2
> $AMBERHOME/exe/parmchk -i lig_h.mol2 -f mol2 -o lig_h.frcmod
> $AMBERHOME/exe/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.gaff
>
$AMBERHOME/exe has not been a directory in Amber since Amber 10, I believe
(maybe Amber 11). So unless you made a link to the bin directory, I would
guess you are using a *very* old version of AmberTools. I would highly
recommend upgrading to AmberTools 15 if that is the case.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Sep 18 2015 - 05:00:03 PDT
