AMBER Archive (2009)

Subject: [AMBER] atom types

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I am trying to simulate prot-RNA compolex using ff99SB forcefield. I have
made the required changes in my pdb file as in:
1. I checked for TER between protein and RNA
2. changed RNA bases name FROM a/u/g/c to RA/RU/RG/RC
3. added 5' and 3' to starting and end base of RNA

still my PDB file is giving me many errors. i am attaching my leap log file.
plz help.

-- 
Regards
Deepti Nayar
Structural Biology- Bioinformatics Unit
Institute of Genomics and Integrative Biology (IGIB), Delhi
CSIR
Delhi
e-mail: deeptinayar_at_gmail.com
          deepti.nayar_at_igib.res.in

• text/x-log attachment: leap.log

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