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
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Received on Sun Oct 29 2023 - 23:30:03 PDT
