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-5.9.63
See for instance the LEaP script in R.E.DD.B.:
http://q4md-forcefieldtools.org/REDDB/projects/W-46/script1.ff
# tripos1.mol2
set DMSO.1.C1 type CT
set DMSO.1.H11 type H1
set DMSO.1.H12 type H1
set DMSO.1.H13 type H1
# You might prefer to add your own FF atom types for S2 & O3
set DMSO.1.S2 type SX
set DMSO.1.O3 type OX
set DMSO.1.C4 type CT
set DMSO.1.H41 type H1
set DMSO.1.H42 type H1
set DMSO.1.H43 type H1
or 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-forcefieldtools.org/REDS/faq.php#5 we can take data
from there & regenerate data for you; see:
http://q4md-forcefieldtools.org/REDS/faq.php#22
regards, 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
> within 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: 3138 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: bond <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 bounding 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
> 1.500000 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 468>.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.
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Received on Fri Jun 28 2013 - 00:30:03 PDT
