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MD simulations / Unnatural base pair helical parameters

« on: September 09, 2020, 05:46:09 pm »

Dear Dr. Xiang,

I did a molecular dynamics simulation for DNA with modified base pairs using gromacs. I wanted to analyze base pair parameters for each base pair.

I tried to use 3DNA also, but it also gave errors.
find_pair -p onesb_frame1.pdb allbp_list

handling file <onesb_frame1.pdb>
Match 'IUG' to 'a' for residue IUG    6  on chain   [#6]
    check it & consider to add line 'IUG     a' to file <baselist.dat>
Match 'JSP' to 'u' for residue JSP   19  on chain   [#19]
    check it & consider to add line 'JSP     u' to file <baselist.dat>
missing ' N1 ' atom : residue name 'JSP', chain  , number [  19 ]
missing ' C5 ' atom : residue name 'JSP', chain  , number [  19 ]
Cannot identify RN9/YN1 in [JSP] -- use atom [ C1 ] instead
missing ' N1 ' atom in base ring atoms
missing ' C5 ' atom in base ring atoms
missing ' N1 ' atom : residue name 'JSP', chain  , number [  19 ]


Do let me know how to calculate base pair parameters including major and minor groove parameters. There was one example in your homepage, but its not working in my case.

Thank you very much
Regards
A Shaikh