Dear Amber developers,
I just noticed that the addatomtype section in leaprc.gaff2 does not
include some of the atom types used in gaff2.dat.
I am studying an organic molecule in which some of the C atoms have been
assigned type c6 in GAFF2. I generated prepi and frcmod files in an
old-fashioned way. Then, After loading the prepi and frcmod files in leap,
I loaded the pdb file of this organic molecule. Leap gives a warning
message:
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-N4-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: *-C7-C10-*
+--- With Sp0 - 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: *-N5-C7-*
+--- With Sp3 - 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: *-N5-C11-*
+--- With Sp3 - 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: *-C8-C11-*
+--- With Sp0 - 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: *-N4-C8-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
Then I checked the leaprc.gaff2 file and found no atom type definition for
c6. So I added
addAtomTypes { { "c6" "C" "sp3" } } at the beginning of the leap script,
and the warning message disappeared. Then I compared the prmtop files
generated with and without the addatomtype command in the leap script and
found some differences in fields ATOMIC_NUMBER, RADII, and SCREEN. The
ATOMIC_NUMBER for the c6 atom was -1 without the atomtype definition. I
guess they have no impact on simulations in explicit solvent, but since
RADII and SCREEN parameters are wrong, they may have an impact on
simulations in implicit solvent.
Interestingly, if I use mol2 and frcmod files instead of prepi, frcmod and
pdb files, the warning message does not show up.
The information above should be enough for debugging. If specific input
data/files are required, I would be happy to provide them.
PS: Centos 7, GCC 9, Amber22/AmberTools23 downloaded today, all patches
applied.
With all the best,
Ye
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Received on Mon Apr 01 2024 - 07:30:02 PDT
