Hi,
I have been generating .prmtop and .inpcrd files using the PDB:1KJR. It has
a modified glycan molecule. I did antechamber for the added molecule BEK
and used both the glycam and gaff force field. Then, I am getting this
tleap error. It adds an extra oxygen molecule to the bond between BEK and
GAL. To solve this, I manually added the angle and torsion parameters to
the .frcmod file generated using paramchk2, but it's no help.
bin/teLeap: Error!
Could not find bond parameter for: Cg - n
Building angle parameters.
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
Could not find angle parameter: Cg - Cg - n
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
Could not find angle parameter: Oh - Cg - n
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
Could not find angle parameter: H1 - Cg - n
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
Could not find angle parameter: Cg - n - c
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
Could not find angle parameter: Cg - n - hn
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
Could not find angle parameter: Cg - n - hn
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
Could not find angle parameter: Cg - Cg - n
Building proper torsion parameters.
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
** No torsion terms for Oh-Cg-Cg-n
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
** No torsion terms for H1-Cg-Cg-n
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
** No torsion terms for Cg-Cg-n-c
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
** No torsion terms for Cg-Cg-n-hn
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
** No torsion terms for Cg-Cg-n-hn
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
** No torsion terms for Ho-Oh-Cg-n
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
** No torsion terms for Oh-Cg-n-c
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
** No torsion terms for Oh-Cg-n-hn
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
** No torsion terms for Oh-Cg-n-hn
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
** No torsion terms for H1-Cg-n-c
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
** No torsion terms for H1-Cg-n-hn
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
** No torsion terms for H1-Cg-n-hn
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
** No torsion terms for Oh-Cg-Cg-n
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
** No torsion terms for H1-Cg-Cg-n
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
** No torsion terms for Cg-Cg-n-c
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
** No torsion terms for Cg-Cg-n-hn
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
** No torsion terms for Cg-Cg-n-hn
/home/lucy/software/amber18/amber18/bin/teLeap: Error!
** No torsion terms for Cg-Cg-Cg-n
and here is the input for teleap.
source leaprc.protein.ff14SB
source leaprc.GLYCAM_06j-1
source leaprc.gaff2
source leaprc.water.tip3p
loadamberparams lig.frcmod
loadoff lig.lib
COM = loadpdb com.pdb
bond COM.140.O4 COM.141.C1
bond COM.141.C3 COM.142.N
set default PBRadii mbondi2
saveamberparm COM complex.prmtop complex.inpcrd
solvateoct COM TIP3PBOX 10.0
addIons2 COM Cl- 0
addIons2 COM Na+ 0
saveamberparm COM complex_solv.prmtop complex_solv.inpcrd
savepdb COM complex_solv.pdb
charge COM
quit
Please help me with this.
Thanks in advance
--
*Yours Sincerely*
*Subhasmita Mahapatra*
*Ph.D. Scholar (PMRF)*
*Computational Biophysics Group*
*Department of Biosciences and Biomedical Engineering*
*Indian Institute of Technology, Indore*
*Madhya Pradesh, India (453552)*
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Received on Sat Dec 02 2023 - 05:00:02 PST
