Dear Amber community,
We are trying to add a glycan to a structure using GLYCAM.web. One of the glycosylation sites adds the glycan inward, so we had to manually adjust the torsion angle of the amino acid to make the glycan face outward. Afterwards we used the pdb4amber command to reduce and dry the structure to prepare for tleap. However, when we run the tleap command we get several errors:
/usr/local/amber24/bin/teLeap: Error!
** No torsion terms for atom types: H2-Cg-Cg-H2
for atom H1 at position 3.454453, 26.331451, 6.176339,
atom C1 at position 2.782840, 26.383052, 5.319383,
atom C1 at position -18.770017, -12.176506, -3.108915,
and atom H1 at position -18.262841, -13.064827, -3.488307.
/usr/local/amber24/bin/teLeap: Error!
** No torsion terms for atom types: H2-Cg-Cg-H2
for atom H1 at position -16.095079, -7.418129, -4.797321,
atom C1 at position -16.983025, -7.386920, -4.165913,
atom C1 at position 3.129759, 6.854339, 20.436985,
and atom H1 at position 3.749182, 7.734951, 20.260580.
/usr/local/amber24/bin/teLeap: Error!
** No torsion terms for atom types: H2-Cg-Cg-H2
for atom H1 at position 8.826406, 2.679141, 19.738365,
atom C1 at position 8.148691, 1.871918, 20.016203,
atom C1 at position -17.821246, -18.731666, 7.727446,
and atom H1 at position -17.811185, -19.209582, 8.708148.
Has anyone else run into this problem when adding glycans to their proteins, and if so any advice would be greatly appreciated?
There are the forcefields we are using:
source leaprc.protein.ff19SB
source leaprc.GLYCAM_06j-1
source leaprc.water.opc
When we don't adjust the torsion angle it runs through tleap smoothly, but fails during minimization due to clashes.
Thank you,
Sena
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Received on Tue Aug 06 2024 - 12:00:02 PDT
