Hi,
I have some experience using GAFF, but I never faced this message, and I'd like to know, what's the best way to proceed in similar cases.
During the tleap step I got the following error messages:
/home/fpontes/miniconda3/envs/AmberTools23/bin/teLeap: Error!
Could not find angle parameter for atom types: ny - c2 - nu
for atom N at position 2.397000, 2.221000, -2.435000,
atom C9 at position 2.838000, 0.953000, -2.765000,
and atom N1 at position 2.183000, -0.112000, -2.298000.
/home/fpontes/miniconda3/envs/AmberTools23/bin/teLeap: Error!
Could not find angle parameter for atom types: ny - c6 - oh
for atom N at position 2.397000, 2.221000, -2.435000,
atom C8 at position 1.219000, 2.413000, -1.598000,
and atom O6 at position 1.402000, 3.620000, -0.885000.
/home/fpontes/miniconda3/envs/AmberTools23/bin/teLeap: Error!
Could not find angle parameter for atom types: c6 - ny - c2
for atom C8 at position 1.219000, 2.413000, -1.598000,
atom N at position 2.397000, 2.221000, -2.435000,
and atom C9 at position 2.838000, 0.953000, -2.765000.
/home/fpontes/miniconda3/envs/AmberTools23/bin/teLeap: Warning!
There are missing parameters.
But these angles are present in frcmod file:
Two of them in an inverse sequence as declared in tleap step:
ny-c2-nu > nu-c2-ny
c6-ny-c2 > c2ny-c6
And the angle ny-c6-oh appears in this same sequence on frcmod file. The inpcrd and prmtop file were created successfully.
Is there something to do to avoid this error message? Can I proceed to my MD ?
Just an extra information: I download the structure of my ligand from Chem Spider, run an protonation assignment in Marvin Sketch and saved as mol2.
Furthermore, I used antechamber to assign bcc charges and gaff2 atom types...
*
antechamber -i TTX_min.mol2 -fi mol2 -o TTX_new.mol2 -fo mol2 -c bcc -j 4 -at gaff2 -nc 1 -m 1 -pf y -rn TTX
And parmchk2 to create the frcmod file:
*
parmchk2 -i TTX_new.mol2 -o TTX.frcmod -f mol2 -a y
Thanks in advance,
Fred
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Received on Mon Jul 29 2024 - 15:00:02 PDT
