Hello everyone,
I am trying to simulate a mutated DNA system. I have created the parameters
for the non-standard residue 8OG (8-oxoguanine). I have the mol2 and frcmod
files prepared for it. However, when I use the bond command in tleap for
forming bonds between adjacent residues, it gives a warning...
>From leap.log
/usr/local/PROGRAMS/amber20/bin/teLeap: Warning!
One sided connection. Residue (8OG) missing connect0 atom.
/usr/local/PROGRAMS/amber20/bin/teLeap: Warning!
One sided connection. Residue (default_name) missing connect1 atom.
Starting new chain with OPC
Starting new chain with OPC
Starting new chain with OPC
Starting new chain with OPC
Starting new chain with OPC
Starting new chain with OPC
Starting new chain with OPC
Starting new chain with OPC
Starting new chain with OPC
Starting new chain with OPC
Starting new chain with OPC
total atoms in file: 3373
Leap added 2480 missing atoms according to residue templates:
53 Heavy
2427 H / lone pairs
> bond MOL.335.O3' MOL.336.P
> bond MOL.336.O3' MOL.337.P
> charge MOL
Total unperturbed charge: -27.824
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
8OG 1
CGLN 1
NGLY 1
WAT 12
)
(no restraints)
> quit
Quit
Exiting LEaP: Errors = 0; Warnings = 8; Notes = 1.
tleap exits with no errors. However the said bonds are neither reflecting
in the pdb generated by teap nor in the subsequent MD simulation.
I request the members to guide me through this problem.
Thanks and regards,
Vaibhav Bhatt
Ph.D Scholar,
Molecular Simulation Lab,
Shiv Nadar IoE,
Greater Noida,
Uttar Pradesh,
India.
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Received on Tue May 21 2024 - 02:30:02 PDT
