AMBER Archive (2009)

Subject: [AMBER] loading RNA sequence in xleap

From: gunajyoti das (guna_das78_at_yahoo.co.in)
Date: Thu Sep 17 2009 - 03:27:49 CDT

hello amber users,
          I tried to load a double stranded tRNA sequence having a minor RNA base INOSINE ( the sequence had been taken from pdb 1XNQ) in xleap. I used leaprc.rna.ff02 force field to start xleap, but unfortunately xleap could not recognise the INOSINE residue. I even loaded the all_modrna.ff08.lib, hoping that the situation will improve, INOSINE still remained unrecognised by xleap.
         
          When I tried loading another double stranded RNA sequence having all standard residues ( G and C), I could easily generate the prmtop and inpcrd files.  
  
          Am I choosing a wrong force field for the INOSINE containing sequence?
  
          Kindly help me out.
     
          with regards, thanking in advance.
 
    Gunajyoti
    Neh university  

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