As the output states, your 8OG is not set up properly. you might want to
share that library if you would like help checking it.
also, don't use a pdb file to check bonds, use the prmtop file. You can use
parmed to list bonds, or you can load the mrptop into a program like VMD
and the actual bond list will be used. If you use a pdb, then the bond
algorithm is usually distance-based on does not tell you what is present in
the prmtop.
On Tue, May 21, 2024, 5:15 AM Vaibhav Bhatt via AMBER <amber.ambermd.org>
wrote:
> 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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>
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Received on Tue May 21 2024 - 07:30:02 PDT
