Dear Users,
I have a PDB file of RNA crystal structure. The resolution is quite high,
so there are ANISOU entries as well. Apart from that, it also has MG and
Water molecules. I have removed all the ANISOU entries as well as
unnecessary water molecules and ions. I have renumbered the atom names as
well as residues using "pdbset" command of CCP4 suite. After applying all
the necessary steps to clean up the PDB as mentioned in AmberTools12
tutorial, when i am trying to load this pdb into tleap (using ff10 force
field), i am getting the following message :
Unknown residue: C number: 0 type: Terminal/beginning
..relaxing end constraints to try for a dbase match
-no luck
Unknown residue: G number: 1 type: Nonterminal
Unknown residue: C number: 2 type: Nonterminal
Unknown residue: G number: 3 type: Nonterminal
Unknown residue: G number: 4 type: Nonterminal
Unknown residue: C number: 5 type: Nonterminal
Unknown residue: A number: 6 type: Nonterminal
Unknown residue: C number: 7 type: Nonterminal
Unknown residue: C number: 8 type: Nonterminal
Unknown residue: G number: 9 type: Nonterminal
Unknown residue: U number: 10 type: Nonterminal
Unknown residue: C number: 11 type: Nonterminal
Unknown residue: C number: 12 type: Nonterminal
Unknown residue: G number: 13 type: Nonterminal
Unknown residue: C number: 14 type: Nonterminal
Unknown residue: G number: 15 type: Nonterminal
Unknown residue: G number: 16 type: Nonterminal
Unknown residue: A number: 17 type: Nonterminal
Unknown residue: A number: 18 type: Nonterminal
Unknown residue: C number: 19 type: Nonterminal
Unknown residue: A number: 20 type: Nonterminal
Unknown residue: A number: 21 type: Nonterminal
Unknown residue: A number: 22 type: Nonterminal
Unknown residue: C number: 23 type: Nonterminal
Unknown residue: G number: 24 type: Nonterminal
Unknown residue: G number: 25 type: Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
I removed terminal phosphate group and renamed Magnesium ions according to
ff10 nomenclature. Why is it giving this message?
Thanks
Asmi
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Received on Tue May 15 2012 - 00:30:04 PDT
