Dear Amber Users,
I have a
pdb file of a protein which has residue name "MOL" for each residue.
When I tried to load it in xleap with force field ff99SB following lines appeared in the xleap window. Will you please let me know how should I
proceed to avoid this problem.
.Matching PDB residue names to LEaP variables.
(Residue 0: MOL, Terminal/last, was not found in name map.)
Unknown residue: MOL number: 0 type:
Terminal/last
..relaxing end constraints to try for a dbase match
-no luck
Creating new UNIT for residue: MOL sequence: 1
Created a new atom named: N3 within residue: .R<MOL 1>
Created a new atom named: C7 within residue: .R<MOL 1>
Created a new atom named: O2 within residue: .R<MOL 1>
Created a new atom named: C1 within residue: .R<MOL 1>
Created a new atom named: N1 within residue: .R<MOL 1>
Created a new atom named: C4 within residue: .R<MOL 1>
Created a new atom named: C3 within residue: .R<MOL 1>
Created a new atom named: C2 within residue: .R<MOL 1>
Created a new atom named: H1 within residue: .R<MOL 1>
Created a new atom named: H2 within residue: .R<MOL 1>
Created a new atom named: H3 within residue: .R<MOL 1>
Created a new atom named: H4 within residue: .R<MOL 1>
Created a new atom named: H5 within residue: .R<MOL
1>
Created a new atom named: H6 within residue: .R<MOL 1>
Created a new atom named: C5 within residue: .R<MOL 1>
Created a new atom named: O1 within residue: .R<MOL 1>
Created a new atom named: C6 within residue: .R<MOL 1>
Created a new atom named: N2 within residue: .R<MOL 1>
Created a new atom named: C11 within residue: .R<MOL 1>
Created a new atom named: O3 within residue: .R<MOL 1>
Created a new atom named: C9 within residue: .R<MOL 1>
Created a new atom named: N4 within residue: .R<MOL 1>
Created a new atom named: C18 within residue: .R<MOL 1>
Created a new atom named: O5 within residue: .R<MOL 1>
Created a new atom named: C17 within residue: .R<MOL 1>
Created a new atom named: N6 within residue: .R<MOL 1>
Created a new atom named: C26 within residue: .R<MOL 1>
Created a new atom named: O7 within residue: .R<MOL
1>
Created a new atom named: C23 within residue: .R<MOL 1>
Created a new atom named: N8 within residue: .R<MOL 1>
Created a new atom named: C34 within residue: .R<MOL 1>
Created a new atom named: O8 within residue: .R<MOL 1>
Created a new atom named: C31 within residue: .R<MOL 1>
Created a new atom named: N9 within residue: .R<MOL 1>
Created a new atom named: O10 within residue: .R<MOL 1>
Created a new atom named: C47 within residue: .R<MOL 1>
Created a new atom named: N11 within residue: .R<MOL 1>
Created a new atom named: H70 within residue: .R<MOL 1>
Created a new atom named: H71 within residue: .R<MOL 1>
Created a new atom named: H72 within residue: .R<MOL 1>
Created a new atom named: C48 within residue: .R<MOL 1>
Created a new atom named: C49 within residue: .R<MOL 1>
Created a new atom named: O11 within residue:
.R<MOL 1>
Created a new atom named: O12 within residue: .R<MOL 1>
Created a new atom named: H67 within residue: .R<MOL 1>
Created a new atom named: H68 within residue: .R<MOL 1>
Created a new atom named: H69 within residue: .R<MOL 1>
Created a new atom named: H66 within residue: .R<MOL 1>
Created a new atom named: C35 within residue: .R<MOL 1>
Created a new atom named: C40 within residue: .R<MOL 1>
Created a new atom named: C44 within residue: .R<MOL 1>
Created a new atom named: N10 within residue: .R<MOL 1>
Created a new atom named: C50 within residue: .R<MOL 1>
Created a new atom named: N12 within residue: .R<MOL 1>
Created a new atom named: H63 within residue: .R<MOL 1>
Created a new atom named: H64 within residue: .R<MOL 1>
Created a new atom named: N13 within residue: .R<MOL 1>
Created a new atom named: H61 within
residue: .R<MOL 1>
Created a new atom named: H62 within residue: .R<MOL 1>
Created a new atom named: H60 within residue: .R<MOL 1>
Created a new atom named: H58 within residue: .R<MOL 1>
Created a new atom named: H59 within residue: .R<MOL 1>
Created a new atom named: H56 within residue: .R<MOL 1>
Created a new atom named: H57 within residue: .R<MOL 1>
Created a new atom named: H54 within residue: .R<MOL 1>
Created a new atom named: C32 within residue: .R<MOL 1>
Created a new atom named: H46 within residue: .R<MOL 1>
Created a new atom named: H47 within residue: .R<MOL 1>
Created a new atom named: H48 within residue: .R<MOL 1>
Created a new atom named: C33 within residue: .R<MOL 1>
Created a new atom named: H49 within residue: .R<MOL 1>
Created a new atom named: H50 within residue: .R<MOL 1>
Created a new atom named: H51
within residue: .R<MOL 1>
Created a new atom named: H45 within residue: .R<MOL 1>
Created a new atom named: H52 within residue: .R<MOL 1>
Created a new atom named: H44 within residue: .R<MOL 1>
Created a new atom named: C24 within residue: .R<MOL 1>
Created a new atom named: C28 within residue: .R<MOL 1>
Created a new atom named: C38 within residue: .R<MOL 1>
Created a new atom named: C42 within residue: .R<MOL 1>
Created a new atom named: C46 within residue: .R<MOL 1>
Created a new atom named: O9 within residue: .R<MOL 1>
Created a new atom named: H42 within residue: .R<MOL 1>
Created a new atom named: C43 within residue: .R<MOL 1>
Created a new atom named: C39 within residue: .R<MOL 1>
Created a new atom named: H39 within residue: .R<MOL 1>
Created a new atom named: H41 within residue: .R<MOL 1>
Created a new atom
named: H40 within residue: .R<MOL 1>
Created a new atom named: H38 within residue: .R<MOL 1>
Created a new atom named: H36 within residue: .R<MOL 1>
Created a new atom named: H37 within residue: .R<MOL 1>
Created a new atom named: H43 within residue: .R<MOL 1>
Created a new atom named: H26 within residue: .R<MOL 1>
Created a new atom named: C10 within residue: .R<MOL 1>
Created a new atom named: C14 within residue: .R<MOL 1>
Created a new atom named: C20 within residue: .R<MOL 1>
Created a new atom named: H21 within residue: .R<MOL 1>
Created a new atom named: C16 within residue: .R<MOL 1>
Created a new atom named: H17 within residue: .R<MOL 1>
Created a new atom named: H18 within residue: .R<MOL 1>
Created a new atom named: H19 within residue: .R<MOL 1>
Created a new atom named: H16 within residue: .R<MOL 1>
Created a
new atom named: H25 within residue: .R<MOL 1>
Created a new atom named: H15 within residue: .R<MOL 1>
Created a new atom named: C8 within residue: .R<MOL 1>
Created a new atom named: C13 within residue: .R<MOL 1>
Created a new atom named: N5 within residue: .R<MOL 1>
Created a new atom named: C27 within residue: .R<MOL 1>
Created a new atom named: N7 within residue: .R<MOL 1>
Created a new atom named: C21 within residue: .R<MOL 1>
Created a new atom named: H10 within residue: .R<MOL 1>
Created a new atom named: H12 within residue: .R<MOL 1>
Created a new atom named: H13 within residue: .R<MOL 1>
Created a new atom named: H11 within residue: .R<MOL 1>
Created a new atom named: H8 within residue: .R<MOL 1>
Created a new atom named: H9 within residue: .R<MOL 1>
Created a new atom named: H14 within residue: .R<MOL 1>
Created
a new atom named: H7 within residue: .R<MOL 1>
Created a new atom named: H35 within residue: .R<MOL 1>
Created a new atom named: C12 within residue: .R<MOL 1>
Created a new atom named: C19 within residue: .R<MOL 1>
Created a new atom named: O4 within residue: .R<MOL 1>
Created a new atom named: O6 within residue: .R<MOL 1>
Created a new atom named: H34 within residue: .R<MOL 1>
Created a new atom named: C15 within residue: .R<MOL 1>
Created a new atom named: H27 within residue: .R<MOL 1>
Created a new atom named: H28 within residue: .R<MOL 1>
Created a new atom named: C22 within residue: .R<MOL 1>
Created a new atom named: C30 within residue: .R<MOL 1>
Created a new atom named: C37 within residue: .R<MOL 1>
Created a new atom named: H32 within residue: .R<MOL 1>
Created a new atom named: H30 within residue: .R<MOL
1>
Created a new atom named: C29 within residue: .R<MOL 1>
Created a new atom named: H29 within residue: .R<MOL 1>
Created a new atom named: C36 within residue: .R<MOL 1>
Created a new atom named: H33 within residue: .R<MOL 1>
total atoms in file: 147
The file contained 147 atoms not in residue templates
Thanking you in advance
Sincerely,
Shubhadip Das
Research Scholar
IIT Guwahati
India
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Received on Fri Nov 30 2012 - 23:30:03 PST
