That seems odd, existence of parameters should not depend on thr initial
coordinates. You likely need to contact the gmycam developers to resolve
the parameter issue, but I wonder if rotating the bond changed anything
other than coordinates. Maybe you could compare the pdb files to confirm no
other changes other than xyz values. Make sure you carry out the identical
reduce etc steps on both pdb files.
Another option might be to build the structure that leads to the min
failure, but then rotate that structure buy retain the prmtop file and use
it with the rotated coordinates.
On Tue, Aug 6, 2024, 2:55 PM Cinar, Sena via AMBER <amber.ambermd.org>
wrote:
> 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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>
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Received on Tue Aug 06 2024 - 13:00:03 PDT
