Hi,
Actually, residue name and atoms name of glycan molecule in PDB file are not match with glycam force field. If you want to build glycoprotein, you should modify it manually before using tleap. I think it's very difficult to make changes manually, I recommend you to use GLYCAM-Web | Utilities for molecular modeling of carbohydrates<
https://glycam.org/> to build a glycoprotein system with glycam force field.
Kind Regards,
Jiafan Guo
________________________________
发件人: SUBHASMITA MAHAPATRA MAHAPATRA via AMBER <amber.ambermd.org>
发送时间: 2023年12月2日 20:46
收件人: amber.ambermd.org <amber.ambermd.org>
主题: [AMBER] teLeap: Error! Could not find angle parameter
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 - 05:30:02 PST
