Hi Amber users,
I tried to parameterize an organic molecule that is covalently linked to Cys. I treated the Cys and the organic molecule together as a whole new molecule (Cys-mol), and parameteried it using GAFF2. The N and C terminus of CYS are connected to LEU and GLY respectively. When I included the CYS-mol in the protein, I used the comannd "bond" to make connections between mol-CYS to LEU and GLY. When checking the system, tleap complains that there are two missing angle parameters. However, the three atoms that form the angle are not connected. Specifically, they are C(cys)-N(LEU)-C(GLY). The C(cys)-N(LEU) are connected (defined by the bond command), but C(GLY) connects with the N terminus of CYS, and it has no connection to LEU. Similarly, the other missing one is N(cys)-C(Gly)-N(LEU). Any suggestion? Thanks!
Best wishes
Peng
Here is the tleap input (1 is LEU and 3 is GLY)
source leaprc.protein.ff19SB
source leaprc.gaff2
CC1 = loadmol2 CC1.mol2
loadamberparams CC1.frcmod
mol = loadpdb CC1.pdb
bond mol.1.C mol.2.N70
bond mol.2.C71 mol.3.N
check mol
The tleap output
/home/software/amber24_cpu_old/bin/teLeap: Error!
Could not find angle parameter for atom types: C - N - C
for atom C71 at position 14.716000, 23.717000, 7.310000,
atom N at position 14.960000, 23.417000, 6.018000,
and atom C at position 11.629000, 24.072000, 8.312000.
/home/software/amber24_cpu_old/bin/teLeap: Error!
Could not find angle parameter for atom types: N - C - N
for atom N70 at position 12.860000, 24.535000, 8.612000,
atom C at position 11.629000, 24.072000, 8.312000,
and atom N at position 14.960000, 23.417000, 6.018000.
/home/software/amber24_cpu_old/bin/teLeap: Warning!
There are missing parameters.
check: Warnings: 57
Unit is OK
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Received on Sun Aug 18 2024 - 14:30:02 PDT
