Hi All.
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 Wed Jun 12 2013 - 19:00:02 PDT
