Dear Dongshan Wei,
> 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.
GAMESS or Firefly/PC-GAMESS or Gaussian.
> But I have neither
> Games nor Gaussian at hand.
R.E.D.
http://q4md-forcefieldtools.org/RED/ should do the job; no need
to prepare the inputs for the QM program...
Just prepare the input file for R.E.D.; i.e. a pseudo PDB file...
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#1
You could also use R.E.D. Server
http://q4md-forcefieldtools.org/REDS/
which provides all the hardware & software required for charge
derivation & force field library building...
> 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.
See first: http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#1
Then you have to extract the modified residue(s) from the PDB file; no
need of sophisticated code here:
'grep XXX 2TRX.pdb > XXX.pdb' i.e. UNIX commands should do the job
XXX is the residue name to be extracted; you could associate this
residue name with the residue number to select more efficiently the
residue to be extracted.
then, you need to cap this (central) fragment with the ACE & NME
chemical group using a Java applet of R.E.D. Server, or the LEaP
program or any builder; save the results to the PDB file format.
You are ready to convert this PDB file into P2N using Ante_R.E.D. and
then to run R.E.D. using this P2N file to get a mol2 file which will
be loaded in LEaP...
See
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#15
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#16
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#17
then: http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
&
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25
Do not hesitate to ask more questions if something is not clear...
regards, Francois
> 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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Received on Fri Jun 21 2013 - 05:00:02 PDT
