Dear Yeping Sun,
It looks like you did not use Ante_R.E.D. 2.0; chemical equivalencing
is not correctly performed: The charges are all but correct when one
wishes to use them in MD simulation.
I would use R.E.D. Server; first Ante_R.E.D. 2.0 and then R.E.D. III.x
or R.E.D. IV.
I let you know what we get with R.E.D. Python...
regards, Francois
> Thank you for your explanation. According to your instruction, I use
> antechamber -i G39_H.pdb -fi pdb -o G39_H.mol2 -fo mol2 -c bcc
> to produce the mol2 file, and then use
> parmchk -i G39_H.mol2 -f mol2 -o frcmod
> to produce the frcmod file. This time the G39_H.mole file seems to
> have atom types in it. Next I use
> tleap -s -f leap.in
> the leap.in file is:
> source leaprc.gaffsource leaprc.ff10leaprc.ff03.r1loadamberparams
> frcmodMOL = loadmol2 G39_H.mol2comp = loadpdb
> 3cl0_H274Y_N1_H_SG_noh.pdbbond comp.92.SG comp.417.SGbond
> comp.124.SG comp.129.SGbond comp.183.SG comp.230.SGbond comp.232.SG
> comp.237.SGbond comp.91.SG comp.417.SGbond comp.124.SG
> comp.129.SGbond comp.183.SG comp.230.SGbond comp.232.SG
> comp.237.SGbond comp.278.SG comp.291.SGbond comp.91.SG
> comp.417.SGbond comp.280.SG comp.289.SGbond comp.318.SG
> comp.336.SGbond comp.421.SG comp.447.SGsolvatebox comp TIP3PBOX
> 10.0addions comp Na+ 0saveoff comp 3cl0.offsaveamberparm comp
> 3cl0.prmtop 3cl0.inpcrdquit
> But I still get the error message (please see leap.log);
> Fatal: Atom .R<G39 469>.A<C1 1> does not have a type
> ....................................................................................................
> FATAL: Atom .R<G39 469>.A<N4 20> does not have a type.
>
> I suspect that leap convert the original numbering of the ligand,
> G39, from 800 to 469, so I change the G39 numbering from 800 to 469
> in the pdb file (3cl0_H274Y_N1_H_SG_noh.pdb) and save the new file
> as 3cl0_H274Y_N1_H_SG_noh.pdb, and change the G39 numbering from 800
> to 469 in the mol2 file and save the new mol2 file as
> G39_H_mod.mol2, and change the input names of the pdb and mol2 files
> in leap.in accordingly and save the new file as leap_mod.in.
> However, I get new error message "Illegal CONECT record in pdb
> file". Please see leap_mod.log)
> The files including 3cl0_H274Y_N1_H_SG_noh.pdb,
> 3cl0_H274Y_N1_H_SG_noh_mod.pdb, G39_H.pdb, G39_H.mol2, frcmod,
> G39_H_mod.mol2, leap.in, leap_mod.in, leap.log, leap_mod.log are
> included in the attachment.
> Could you help me with it? Thank you!
>
> Sincerely,
> Yeping Sun
> ------------------------------------------------------------------????FyD<fyd.q4md-forcefieldtools.org>?????2013?6?28? 15:04????AMBER Mailing List<amber.ambermd.org>;????Re: [AMBER] FATAL: Atom XXX does not have a type Dear Yeping Sun,R.E.D. III.x or R.E.D. IV (Perl) does _not_ perform atom typing (R.E.D. Python does). You need to define the atom types in the mol2 file...Let's take an example in R.E.DD.B.http://q4md-forcefieldtools.org/REDDB/projects/W-1/The mol2 file:http://q4md-forcefieldtools.org/REDDB/projects/W-1/tripos1.mol2.<TRIPOS>ATOM 1 C1 1.352237 -0.856933 0.225852 C 1 DMSO -0.2897 **** 2 H11 1.336243 -1.843530 -0.221408 H 1 DMSO 0.1284 **** 3 H12 1.276947 -0.923392 1.304085 H 1 DMSO 0.1284 **** 4 H13 2.275139 -0.356278 -0.035153 H 1 DMSO 0.1284 **** 5 S2 -0.000004 0.136959 -0.414455 S 1 DMSO 0.3177 **** 6 O3 -0.000040 1.405694 0.357557 O 1 DMSO -0.5085 **** 7 C4 -1.352189 -0.857006 0.225851 C 1 DMSO -0.2897 **** 8 H41 -2.275117 -0.356396 -0.035149 H 1 DMSO 0.1284 ****
> 9
> H42 -1.336143 -1.843599 -0.221415 H 1 DMSO 0.1284 **** 10 H43
> -1.276895 -0.923466 1.304085 H 1 DMSO 0.1284 **** ^^^^^ ** here as
> you can see the chemical elements have to be replaced by the atom
> types; i.e. in this case:.<TRIPOS>ATOM 1 C1 1.352237 -0.856933
> 0.225852 CT 1 DMSO -0.2897 **** 2 H11 1.336243 -1.843530 -0.221408
> H1 1 DMSO 0.1284 **** 3 H12 1.276947 -0.923392 1.304085 H1 1 DMSO
> 0.1284 **** 4 H13 2.275139 -0.356278 -0.035153 H1 1 DMSO 0.1284 ****
> 5 S2 -0.000004 0.136959 -0.414455 S 1 DMSO 0.3177 **** 6 O3
> -0.000040 1.405694 0.357557 O 1 DMSO -0.5085 **** 7 C4 -1.352189
> -0.857006 0.225851 CT 1 DMSO -0.2897 **** 8 H41 -2.275117 -0.356396
> -0.035149 H1 1 DMSO 0.1284 **** 9 H42 -1.336143 -1.843599 -0.221415
> H1 1 DMSO 0.1284 **** 10 H43 -1.276895 -0.923466 1.304085 H1 1 DMSO
> 0.1284 ****You could do that using the 'set' command on the LEaP
> program:See
> http://ambermd.org/doc6/html/AMBER-sh-5.9.html#sh-5.9.63See for
> instance the LEaP script in R.E.DD.B.: http://q4md-forcefieldtool
> s.org/REDDB/projects/W-46/script1.ff# tripos1.mol2set DMSO.1.C1 type
> CTset DMSO.1.H11 type H1set DMSO.1.H12 type H1set DMSO.1.H13 type
> H1# You might prefer to add your own FF atom types for S2 & O3set
> DMSO.1.S2 type SXset DMSO.1.O3 type OXset DMSO.1.C4 type CTset
> DMSO.1.H41 type H1set DMSO.1.H42 type H1set DMSO.1.H43 type H1or I
> guess you can use Antechamber to load the mol2 file generated by
> R.E.D. without atom types and output another mol2 file with atom
> types...you could also send us your R.E.D. job as well (replacing
> the .com gaussian input by .com.txt to avoid problems with mail
> servers) so that we run the Re-fit mode of R.E.D. Python to generate
> a mol3 file with residue connection (if needed), atom types, charges
> corrected for rounding error errors with frcmod files, we can add
> lone pairs and extra-points, united carbons, etc...if you used
> R.E.D. Server just request a private assistance from the web site &
> provide the PXXXX R.E.D. Server job name.See http://q4md-forcefieldtoo
> ls.org/REDS/faq.php#5 we can take data from there & regenerate data
> for you; see:http://q4md-forcefieldtools.org/REDS/faq.php#22regards,
> Francois> I am trying to prepare the input files for amber
> simulation on a > protein-ligand. The ligand is named G39 in the pdb
> file. I used > R.E.D. server to generate the mol2 file
> (Mol_m1-o1.mol2) and then > used parmchk to produce the frcmod
> file. Next I tried to use tleap, > and the leap.in file is:> source
> leaprc.gaffsource leaprc.ff10loadamberparams frcmodMOL = > loadmol2
> Mol_m1-o1.mol2comp = loadpdb complex.pdbbond comp.92.SG >
> comp.417.SGbond comp.124.SG comp.129.SGbond comp.183.SG >
> comp.230.SGbond comp.232.SG comp.237.SGbond comp.91.SG >
> comp.417.SGbond comp.124.SG comp.129.SGbond comp.183.SG >
> comp.230.SGbond comp.232.SG comp.237.SGbond comp.278.SG >
> comp.291.SGbond comp.91.SG comp.417.SGbond comp.280.SG >
> comp.289.SGbond comp.318.SG comp.336.SGbond comp.421.SG >
> comp.447.SGsolvatebox comp TIP3PBOX 10.0addions comp Na+ 0saveoff >
> comp
> 3cl0.offsaveamberparm comp 3cl0.prmtop 3cl0.inpcrdquit> > However,
> when I run tleap -s -f leap.in, I get the follow output:> Loading
> parameters: ./frcmodReading force field modification type > file
> (frcmod)Reading title:remark goes hereLoading Mol2 file: >
> ./Mol_m1-o1.mol2Reading MOLECULE named G39Loading PDB file: >
> ./3cl0_H274Y_N1_H_SG_noh.pdbUnknown residue: CA number: 385 >
> type: NonterminalUnknown residue: G39 number: 386 type: >
> NonterminalCreated a new atom named: OXT within residue: .R<ILE >
> 467>Creating new UNIT for residue: CA sequence: 468One sided >
> connection. Residue: missing connect0 atom.Created a new atom >
> named: CA within residue: .R<CA 468>Creating new UNIT for residue: >
> G39 sequence: 469Created a new atom named: C1 within residue: .R<G39
> > 469>Created a new atom named: O1A within residue: .R<G39
> 469>Created > a new atom named: O1B within residue: .R<G39
> 469>Created a new atom > named: C2 within residue: .R<G39
> 469>Created a new atom named: C3 > with
> in residue: .R<G39 469>Created a new atom named: C4 within >
> residue: .R<G39 469>Created a new atom named: C5 within residue: >
> .R<G39 469>Created a new atom> named: N5 within residue: .R<G39
> 469>Created a new atom named: C10 > within residue: .R<G39
> 469>Created a new atom named: O10 within > residue: .R<G39
> 469>Created a new atom named: C11 within residue: > .R<G39
> 469>Created a new atom named: C6 within residue: .R<G39 >
> 469>Created a new atom named: C7 within residue: .R<G39 469>Created
> > a new atom named: O7 within residue: .R<G39 469>Created a new atom
> > named: C8 within residue: .R<G39 469>Created a new atom named: C9
> > within residue: .R<G39 469>Created a new atom named: C81 within >
> residue: .R<G39 469>Created a new atom named: C82 within residue: >
> .R<G39 469>Created a new atom named: C91 within residue: .R<G39 >
> 469>Created a new atom named: N4 within residue: .R<G39 469> total
> > atoms in file: 3161 Leap added 3138 missing atoms according to >
> residue templates: 3
> 138 H / lone pairs The file contained 22 > atoms not in residue
> templatesbond: Argument #1 is type String must > be of type:
> [atom]usage: bond <atom1> <atom2> [order]bond: Argument > #1 is
> type String must be of type: [atom]usage: bond <atom1> > <atom2>
> [order]bond: Argument #1 is type String must be of type: >
> [atom]usage: bond <atom1> <atom2> [order]bond: Argument #1 is type
> > String must be of type: [atom]usage: bond <atom1> <atom2> >
> [order]bond: Argument #1 is type String must be of type: >
> [atom]usage: bond <atom1> <atom2> [order]bond: Argument #1 is type
> > String must be of type: [atom]usage: bond <atom1> <atom2> >
> [order]bond: Argument #1 is type String must be of type: >
> [atom]usage: bond <atom1> <atom2> [order]bond: Argument #1 is type
> > String must be of type: [atom]usage: bond <atom1> <atom2> >
> [order]bond: Argument #2 is type String must be of type: >
> [atom]usage: bond <atom1> <atom2> [order]bond: Argument #2 is type
> > String must be of type: [atom]usage: bo
> nd <atom1> <atom2> > [order] (using default radius 1.500000 for
> OXT) (using default > radius 1.500000 for CA) (using default radius
> 1.500000 for > C1) (using default radius 1.500000 for O1A) (using
> default radius > 1.500> 000 for O1B) (using default radius 1.500000
> for C2) (using default > radius 1.500000 for C3) (using default
> radius 1.500000 for > C4) (using default radius 1.500000 for
> C5) (using default radius > 1.500000 for N5) (using default radius
> 1.500000 for C10) (using > default radius 1.500000 for O10) (using
> default radius 1.500000 for > C11) (using default radius 1.500000
> for C6) (using default radius > 1.500000 for C7) (using default
> radius 1.500000 for O7) (using > default radius 1.500000 for
> C8) (using default radius 1.500000 for > C9) (using default radius
> 1.500000 for C81) (using default radius > 1.500000 for C82) (using
> default radius 1.500000 for C91) (using > default radius 1.500000
> for N4) Solute vdw bounding > box: 57.502 57.677
> 61.240 Total bou
> nding box for atom > centers: 77.502 77.677 81.240 Solvent unit >
> box: 18.774 18.774 18.774 (using default radius
> > 1.500000 for OXT) (using default radius 1.500000 for CA) (using >
> default radius 1.500000 for C1) (using default r> adius 1.500000 for
> O1A) (using default radius 1.500000 for > O1B) (using default radius
> 1.500000 for C2) (using default radius > 1.500000 for C3) (using
> default radius 1.500000 for C4) (using > default radius 1.500000 for
> C5) (using default radius 1.500000 for > N5) (using default radius
> 1.500000 for C10) (using default radius > 1.500000 for O10) (using
> default radius 1.500000 for C11) (using > default radius 1.500000
> for C6) (using default radius 1.500000 for > C7) (using default
> radius 1.500000 for O7) (using default radius > 1.500000 for
> C8) (using default radius 1.500000 for C9) (using > default radius
> 1.500000 for C81) (using default radius 1.500000 for > C82) (using
> default radius 1.500000 for C91) (using default radius > 1.50
> 0000 for N4) Total vdw box size: 80.756 > 81.019
> 84.432 angstroms. Volume: 552415.997 A^3 Mass > 274487.606 >
> amu, Density > 0.825 g/cc (type - hence mass - of one or more
> > atoms could not be found) Added 12722 residues.3 Na+ ions
> required > to neutraliz> e.Using default radius 1.50 for ion
> Na+Adding 3 counter ions to > "comp" using 1A gridUsed default
> radius 1.50 for 22 atomsGrid > extends from solute vdw + 1.50 to
> 7.50Resolution: 1.00 > Angstrom.grid build: 1 secSolvent
> present: replacing closest with > ion when steric overlaps
> occurCalculating grid > chargescharges: 9 sec(Replacing solvent
> molecule)Placed Na+ in comp > at (-22.85, 22.75, 4.56).(No solvent
> overlap)Placed Na+ in comp at > (19.11, -6.61, -17.97).(Replacing
> solvent molecule)Placed Na+ in > comp at (5.85, 31.42, 8.49).Done
> adding ions.Building > topology.Building atom parameters.Checking
> Unit.FATAL: Atom .R<ILE > 467>.A<OXT 20> does not have a
> type.FATAL: Atom .R<CA 46
> 8>.A<CA 1> > does not have a type.FATAL: Atom .R<G39 469>.A<C1 1>
> does not have > a type.FATAL: Atom .R<G39 469>.A<O1A 2> does not
> have a > type.FATAL: Atom .R<G39 469>.A<O1B 3> does not have a
> type.FATAL: > Atom .R<G39 469>.A<C2 4> does not have a type.FATAL:
> Atom .R<G39 > 469>.A<C3 5> does not have a type.FA> TAL: Atom
> .R<G39 469>.A<C4 6> does not have a type.FATAL: Atom > .R<G39
> 469>.A<C5 7> does not have a type.FATAL: Atom .R<G39 > 469>.A<N5 8>
> does not have a type.FATAL: Atom .R<G39 469>.A<C10 9> > does not
> have a type.FATAL: Atom .R<G39 469>.A<O10 10> does not > have a
> type.FATAL: Atom .R<G39 469>.A<C11 11> does not have a >
> type.FATAL: Atom .R<G39 469>.A<C6 12> does not have a type.FATAL:
> > Atom .R<G39 469>.A<C7 13> does not have a type.FATAL: Atom .R<G39
> > 469>.A<O7 14> does not have a type.FATAL: Atom .R<G39 469>.A<C8
> 15> > does not have a type.FATAL: Atom .R<G39 469>.A<C9 16> does
> not have > a type.FATAL: Atom .R<G39 469>.A<C81 17> does not have a
> > type.
> FATAL: Atom .R<G39 469>.A<C82 18> does not have a type.FATAL: >
> Atom .R<G39 469>.A<C91 19> does not have a type.FATAL: Atom .R<G39
> > 469>.A<N4 20> does not have a type.Failed to generate >
> parametersParameter file was not saved. Quit> The ligand,
> G39, is numbered 800 in the original pdb file, but leap > seemed to
> renumber it as 469. Except the difference in G39 > numbering, I
> cannot find any other thing that cause the errors, > Could you help
> me figure it out? Thanks in
> advance._______________________________________________AMBER mailing
> listAMBER.ambermd.orghttp://lists.ambermd.org/mailman/listinfo/amber
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Received on Sat Jun 29 2013 - 03:00:02 PDT
