Dear Dongshan Wei,
the recognition between the PDB file and the FF loaded is based on the
atom and residue names; and in a residue two atoms cannot bear the
same name (so that they can be differentiated).
Observed errors:
-1 duplicate [ CD1] atoms (total 2)
-> See:
> Warning: Atom names in each residue should be unique.
> (Same-name atoms are handled by using the first
> occurrence and by ignoring the rest.
> Frequently duplicate atom names stem from alternate
> conformations in the PDB file.)
-2 Unknown residue: MPD number: 217 type: Nonterminal
it looks like you have an unknown residue: check if this residue in
present in the set of FF libraries you loaded in LEaP; if not you will
have to develop a new library for this new residue/the corresponding
molecular fragment. For that you could use R.E.D. or R.E.D. Server;
See tutorials at:
http://q4md-forcefieldtools.org/Tutorial/
regards, Francois
> I'm an beginner of Amber software. Now I'm using Amber to do a simulation
> about 2TRX protein. I donwloaded the 2TRX.pdb file from the PDB database.
> When I used tleap to create the .prmtop and .inpcrd files, I got error
> information as follows. The error information indicates that tleap cannot
> read the CU and MPD residues. How can I solve the problem?
>
> Thank you in advance!
>
> Dongshan Wei
>
>
> =========================================================
>
> tleap -s -f ~/Amber12/amber12/dat/leap/cmd/oldff/leaprc.ff03
>> m = loadpdb 2TRX.pdb
> Loading PDB file: ./2TRX.pdb
> (starting new molecule for chain B)
> (starting new molecule for chain A)
> (starting new molecule for chain B)
> -- residue 5: duplicate [ C] atoms (total 2)
> -- residue 5: duplicate [ O] atoms (total 2)
> -- residue 6: duplicate [ C] atoms (total 2)
> -- residue 6: duplicate [ CA] atoms (total 2)
> -- residue 6: duplicate [ CB] atoms (total 2)
> -- residue 6: duplicate [ CD2] atoms (total 2)
> -- residue 6: duplicate [ CE1] atoms (total 2)
> -- residue 6: duplicate [ CG] atoms (total 2)
> -- residue 6: duplicate [ N] atoms (total 2)
> -- residue 6: duplicate [ ND1] atoms (total 2)
> -- residue 6: duplicate [ NE2] atoms (total 2)
> -- residue 6: duplicate [ O] atoms (total 2)
> -- residue 7: duplicate [ N] atoms (total 2)
> -- residue 23: duplicate [ CD1] atoms (total 2)
> -- residue 23: duplicate [ CG1] atoms (total 2)
> -- residue 23: duplicate [ CG2] atoms (total 2)
> -- residue 47: duplicate [ CG] atoms (total 2)
> -- residue 47: duplicate [ OD1] atoms (total 2)
> -- residue 47: duplicate [ OD2] atoms (total 2)
> -- residue 48: duplicate [ CD] atoms (total 2)
> -- residue 48: duplicate [ CG] atoms (total 2)
> -- residue 48: duplicate [ OE1] atoms (total 2)
> -- residue 48: duplicate [ OE2] atoms (total 2)
> -- residue 58: duplicate [ CD1] atoms (total 2)
> -- residue 58: duplicate [ CD2] atoms (total 2)
> -- residue 80: duplicate [ CD1] atoms (total 2)
> -- residue 80: duplicate [ CD2] atoms (total 2)
> -- residue 114: duplicate [ C] atoms (total 2)
> -- residue 114: duplicate [ CA] atoms (total 2)
> -- residue 114: duplicate [ CB] atoms (total 2)
> -- residue 114: duplicate [ CD2] atoms (total 2)
> -- residue 114: duplicate [ CE1] atoms (total 2)
> -- residue 114: duplicate [ CG] atoms (total 2)
> -- residue 114: duplicate [ N] atoms (total 2)
> -- residue 114: duplicate [ ND1] atoms (total 2)
> -- residue 114: duplicate [ NE2] atoms (total 2)
> -- residue 114: duplicate [ O] atoms (total 2)
> -- residue 155: duplicate [ CG] atoms (total 2)
> -- residue 155: duplicate [ OD1] atoms (total 2)
> -- residue 155: duplicate [ OD2] atoms (total 2)
> -- residue 166: duplicate [ CD1] atoms (total 2)
> -- residue 166: duplicate [ CD2] atoms (total 2)
> -- residue 188: duplicate [ CD1] atoms (total 2)
> -- residue 188: duplicate [ CD2] atoms (total 2)
>
> Warning: Atom names in each residue should be unique.
> (Same-name atoms are handled by using the first
> occurrence and by ignoring the rest.
> Frequently duplicate atom names stem from alternate
> conformations in the PDB file.)
>
> Unknown residue: CU number: 216 type: Terminal/beginning
> ..relaxing end constraints to try for a dbase match
> -no luck
> Unknown residue: MPD number: 217 type: Nonterminal
> Unknown residue: MPD number: 218 type: Nonterminal
> Unknown residue: MPD number: 219 type: Nonterminal
> Unknown residue: MPD number: 220 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Unknown residue: CU number: 221 type: Terminal/beginning
> ..relaxing end constraints to try for a dbase match
> -no luck
> Unknown residue: MPD number: 222 type: Nonterminal
> Unknown residue: MPD number: 223 type: Nonterminal
> Unknown residue: MPD number: 224 type: Terminal/last
> ..relaxing end constraints to try for a dbase match
> -no luck
> Creating new UNIT for residue: CU sequence: 217
> Created a new atom named: CU within residue: .R<CU 217>
> Creating new UNIT for residue: MPD sequence: 218
> Created a new atom named: C1 within residue: .R<MPD 218>
> Created a new atom named: C2 within residue: .R<MPD 218>
> Created a new atom named: O2 within residue: .R<MPD 218>
> Created a new atom named: CM within residue: .R<MPD 218>
> Created a new atom named: C3 within residue: .R<MPD 218>
> Created a new atom named: C4 within residue: .R<MPD 218>
> Created a new atom named: O4 within residue: .R<MPD 218>
> Created a new atom named: C5 within residue: .R<MPD 218>
> Creating new UNIT for residue: MPD sequence: 219
> Created a new atom named: C1 within residue: .R<MPD 219>
> Created a new atom named: C2 within residue: .R<MPD 219>
> Created a new atom named: O2 within residue: .R<MPD 219>
> Created a new atom named: CM within residue: .R<MPD 219>
> Created a new atom named: C3 within residue: .R<MPD 219>
> Created a new atom named: C4 within residue: .R<MPD 219>
> Created a new atom named: O4 within residue: .R<MPD 219>
> Created a new atom named: C5 within residue: .R<MPD 219>
> Creating new UNIT for residue: MPD sequence: 220
> Created a new atom named: C1 within residue: .R<MPD 220>
> Created a new atom named: C2 within residue: .R<MPD 220>
> Created a new atom named: O2 within residue: .R<MPD 220>
> Created a new atom named: CM within residue: .R<MPD 220>
> Created a new atom named: C3 within residue: .R<MPD 220>
> Created a new atom named: C4 within residue: .R<MPD 220>
> Created a new atom named: O4 within residue: .R<MPD 220>
> Created a new atom named: C5 within residue: .R<MPD 220>
> Creating new UNIT for residue: MPD sequence: 221
> Created a new atom named: C1 within residue: .R<MPD 221>
> Created a new atom named: C2 within residue: .R<MPD 221>
> Created a new atom named: O2 within residue: .R<MPD 221>
> Created a new atom named: CM within residue: .R<MPD 221>
> Created a new atom named: C3 within residue: .R<MPD 221>
> Created a new atom named: C4 within residue: .R<MPD 221>
> Created a new atom named: O4 within residue: .R<MPD 221>
> Created a new atom named: C5 within residue: .R<MPD 221>
> Creating new UNIT for residue: CU sequence: 222
> Created a new atom named: CU within residue: .R<CU 222>
> Creating new UNIT for residue: MPD sequence: 223
> Created a new atom named: C1 within residue: .R<MPD 223>
> Created a new atom named: C2 within residue: .R<MPD 223>
> Created a new atom named: O2 within residue: .R<MPD 223>
> Created a new atom named: CM within residue: .R<MPD 223>
> Created a new atom named: C3 within residue: .R<MPD 223>
> Created a new atom named: C4 within residue: .R<MPD 223>
> Created a new atom named: O4 within residue: .R<MPD 223>
> Created a new atom named: C5 within residue: .R<MPD 223>
> Creating new UNIT for residue: MPD sequence: 224
> Created a new atom named: C1 within residue: .R<MPD 224>
> Created a new atom named: C2 within residue: .R<MPD 224>
> Created a new atom named: O2 within residue: .R<MPD 224>
> Created a new atom named: CM within residue: .R<MPD 224>
> Created a new atom named: C3 within residue: .R<MPD 224>
> Created a new atom named: C4 within residue: .R<MPD 224>
> Created a new atom named: O4 within residue: .R<MPD 224>
> Created a new atom named: C5 within residue: .R<MPD 224>
> Creating new UNIT for residue: MPD sequence: 225
> Created a new atom named: C1 within residue: .R<MPD 225>
> Created a new atom named: C2 within residue: .R<MPD 225>
> Created a new atom named: O2 within residue: .R<MPD 225>
> Created a new atom named: CM within residue: .R<MPD 225>
> Created a new atom named: C3 within residue: .R<MPD 225>
> Created a new atom named: C4 within residue: .R<MPD 225>
> Created a new atom named: O4 within residue: .R<MPD 225>
> Created a new atom named: C5 within residue: .R<MPD 225>
> total atoms in file: 1886
> Leap added 1946 missing atoms according to residue templates:
> 1946 H / lone pairs
> The file contained 58 atoms not in residue templates
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Received on Thu Jun 13 2013 - 01:00:02 PDT
