Hi ET and Francois,
Thanks a lot to you. I will take your advice to set up the unknown residue
libraries first and then use LEaP to create the .prmtop and .inpcrd files.
Dongshan
On Thu, Jun 13, 2013 at 3:37 PM, FyD <fyd.q4md-forcefieldtools.org> wrote:
> 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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>
--
---------------------------------------------------------
Dongshan Wei, Dr.
Chongqing Institute of Green and Intelligent Technology, CAS
85 Jinyu Ave, Yubei Area, Chongqing 401120, China
Email: dswei.cigit.ac.cn <dswei.cigit.cas.cn>
Phone: (+86) 23-63063762
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Received on Thu Jun 13 2013 - 07:00:02 PDT
