Hello,
I am trying to parameterize a small molecule for MD simulations in amber22, but I keep running into a tleap warning where it assigns a number of atoms as 'Sp0' hybridization. The following warning messages come up when I use tleap to ionize and solvate the protein-ligand complex.
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-C12-C10-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-N3-C10-*
+--- With Sp2 - Sp0
...
I do not encounter these warning messages when making the lib file of the small molecule. I performed a geometry optimization for the small molecule in Gaussian16 and then ran a single point energy calculation to get the RESP charges. I created a mol2 file using antechamber and the RESP charges from g16. Then, used parmchk2 to generate the frcmod file. Afterwards, I used the mol2 and frcmod files to saveoff the .lib file.
antechamber -i [g16 file].log -fi gout -o [filename].mol2 -fo mol2 -ao name -at "gaff2" \
-pf y -an y -c resp -nc 0 -rn LIG -ek "ndiis_attempts=700" -j 5
parmchk2 -i [filename].mol2 -o [filename].frcmod -f mol2 -s 2
I confirmed that the hybridization of all atoms that tleap lists as "Sp0" are indeed either sp2 or sp3 hybridization. Is there a tleap command where I can correct the hybridization of specific atoms? The warning message suggests to use addAtomTypes, which I tried to correct the hybridization but it did not resolve the warning messages:
addAtomTypes {
{ "C10" "C" "sp3" }
{ "C12" "C" "sp3" }
{ "N3" "N" "sp2" }
...
}
The topology files of the protein-ligand complex are generated from tLeap, but I'm not sure if I can trust the small molecule torsions/hybridizations. I have used my workflow for other small molecules and have not run into this issue before.
Any help would be greatly appreciated,
Eric
_______________________________________
Eric Hantz
Postdoctoral Research Fellow - Renslo Lab
UCSF - Pharmaceutical Chemistry
Email: eric.hantz.ucsf.edu
Phone: 570-688-8720
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Received on Tue Jun 04 2024 - 13:30:02 PDT
