Hi ET and Francois,
After one week's investigation, I found to create the charges and
connectivity for unknown residues are not a tedious thing. For the charge
deterimantion, it seems that I need to use R.E.D. program combined with the
quantum chemistry calcualtion in Games or Gaussian. But I have neither
Games nor Gaussian at hand. So if you have a mature procedure, could you
please help me create the .protmp and .inpcrd files for the 2TRX protein
molecule? The original pdb file downloaded from pdb database is attached
here.
Thanks so much!
Dongshan
On Thu, Jun 13, 2013 at 9:49 PM, Dongshan Wei <dswei0523.gmail.com> wrote:
> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> ---------------------------------------------------------
> 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
> ---------------------------------------------------------
>
--
---------------------------------------------------------
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 Fri Jun 21 2013 - 02:30:03 PDT
