I don't have suggestions for you, but it might help if you include the
input files as well as just the output pdb and the frcmod.
what PDB file did you read into leap? what is the exact leap input file
that you used? what is the mol2 file?
those are probably the source of the problem, rather than the frcmod file
that you shared.
On Mon, Oct 30, 2023 at 2:24 AM Priyasha Majee via AMBER <amber.ambermd.org>
wrote:
>
>
> Dear All,
>
> I am working with a 22-mer DNA sequence. I have added a modification at
> 12th position and named it as BF. I have obtained the .mol2 file and
> .frcmod file for BF using Gaussian. then using 'Bond' and 'remove'
> command to make bonds as follows
>
> remove hiv.hiv.12.OP1
>
> remove hiv hiv.13.OP1
>
> bond hiv.11.O3' hiv.12.P
>
> bond hiv.12.O3' hiv.13.P
>
> Even after making bonds between the required atoms, I am getting a TER
> card after BF-12 which is creating a break in the DNA. Also I am not
> able to get the prmtop and inpcrd file for this. i am attaching .frcmod
> file of the BF. i cant even use parmed and printBonds to check if there
> is any problem. could anyone please help me out with this.
>
> Thank you in advance
>
> Regards,
>
> Priyasha Majee_______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 30 2023 - 07:30:02 PDT
