hi
I am using amber12 to minimize a modeled beta-cyclodextrin and used
forcefield q4md-cd (combination of glycam04+amber99sb). I want to
build input files (complex beta-cyclodextrin with daidzein). then, I
used from antechamber for building input file topology and coordinate
file.But a new problem: when I want to build topology and coordinate
files for complex, it showed this error;
When I add ions it also showed error in finding vdW
(or other) parameters for type: cc
leap.log
log started: Sat Jan 14 16:30:11 2017
Log file: ./leap.log
>
> # load Amber99SB & only what we need...
> addAtomTypes {
> # Amber
> { "HZ" "H" "sp3" }
> { "H" "H" "sp3" }
> { "HO" "H" "sp3" }
> { "H1" "H" "sp3" }
> { "H2" "H" "sp3" }
> { "HC" "H" "sp3" }
> { "HA" "H" "sp3" }
> { "HW" "H" "sp3" }
> { "OW" "O" "sp3" }
> { "OH" "O" "sp3" }
> { "OS" "O" "sp3" }
> { "O" "O" "sp2" }
> { "O2" "O" "sp2" }
> { "S" "S" "sp3" }
> { "CT" "C" "sp3" }
> { "CZ" "C" "sp3" }
> { "C" "C" "sp2" }
> { "CA" "C" "sp2" }
> { "N" "N" "sp2" }
> { "CL" "Cl" "sp3" }
> # Glycam
> { "CG" "C" "sp3" }
> }
>
> parm99 = loadamberparams parm99.dat
Loading parameters: ./parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
(UNKNOWN ATOM TYPE: HS)
(UNKNOWN ATOM TYPE: H3)
(UNKNOWN ATOM TYPE: HP)
(UNKNOWN ATOM TYPE: H4)
(UNKNOWN ATOM TYPE: H5)
(UNKNOWN ATOM TYPE: C*)
(UNKNOWN ATOM TYPE: C*)
(UNKNOWN ATOM TYPE: C*)
(UNKNOWN ATOM TYPE: C*)
(UNKNOWN ATOM TYPE: C*)
(UNKNOWN ATOM TYPE: C*)
(UNKNOWN ATOM TYPE: C*)
(UNKNOWN ATOM TYPE: C*)
(UNKNOWN ATOM TYPE: C*)
(UNKNOWN ATOM TYPE: C*)
(UNKNOWN ATOM TYPE: C*)
(UNKNOWN ATOM TYPE: C*)
(UNKNOWN ATOM TYPE: C*)
(UNKNOWN ATOM TYPE: C*)
(UNKNOWN ATOM TYPE: N3)
(UNKNOWN ATOM TYPE: NY)
(UNKNOWN ATOM TYPE: SH)
(UNKNOWN ATOM TYPE: P)
(UNKNOWN ATOM TYPE: IM)
(UNKNOWN ATOM TYPE: Li)
(UNKNOWN ATOM TYPE: IP)
(UNKNOWN ATOM TYPE: Na)
(UNKNOWN ATOM TYPE: K)
(UNKNOWN ATOM TYPE: Rb)
(UNKNOWN ATOM TYPE: Cs)
(UNKNOWN ATOM TYPE: MG)
(UNKNOWN ATOM TYPE: C0)
(UNKNOWN ATOM TYPE: Zn)
(UNKNOWN ATOM TYPE: F)
(UNKNOWN ATOM TYPE: Br)
(UNKNOWN ATOM TYPE: I)
(UNKNOWN ATOM TYPE: IB)
(UNKNOWN ATOM TYPE: LP)
> FF99SB = loadamberparams frcmod.ff99SB
Loading parameters: ./frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
>
> loadoff solvents.lib
Loading library: /usr/local/amber12//dat/leap/lib/solvents.lib
Loading: CHCL3BOX
Loading: DC4
Loading: MEOHBOX
Loading: NMABOX
Loading: PL3
Loading: POL3BOX
Loading: QSPCFWBOX
Loading: SPC
Loading: SPCBOX
Loading: SPCFWBOX
Loading: SPF
Loading: SPG
Loading: T4E
Loading: TIP3PBOX
Loading: TIP3PFBOX
Loading: TIP4PBOX
Loading: TIP4PEWBOX
Loading: TIP5PBOX
Loading: TP3
Loading: TP4
Loading: TP5
Loading: TPF
>
> # Use Glycam
> glycam04 = loadamberparams glycam04.dat
Loading parameters: ./glycam04.dat
Reading title:
GLYCAM PARAMETERS (FOR AMBER 8.0, RESP 0.010), COPYRIGHT CCRC 2004
(UNKNOWN ATOM TYPE: CY)
>
> HOH = TP3
> WAT = TP3
>
> #load q4md force field parameters
> Q4MD = loadamberparams frcmod.q4md
Loading parameters: ./frcmod.q4md
Reading force field modification type file (frcmod)
Reading title:
For heterogeneous glycoconjugates
>
> loadamberprep 4GAq4md.prepi
Loading Prep file: ./4GAq4md.prepi
Loaded UNIT: 4GA
> loadamberparams frcmod.ionsjc_tip3p
Loading parameters: /usr/local/amber12//dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham
JPCB (2008)
(UNKNOWN ATOM TYPE: Li+)
(UNKNOWN ATOM TYPE: Na+)
(UNKNOWN ATOM TYPE: K+)
(UNKNOWN ATOM TYPE: Rb+)
(UNKNOWN ATOM TYPE: Cs+)
(UNKNOWN ATOM TYPE: F-)
(UNKNOWN ATOM TYPE: Cl-)
(UNKNOWN ATOM TYPE: Br-)
(UNKNOWN ATOM TYPE: I-)
> loadamberparams DZD.frcmod
Loading parameters: ./DZD.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
> loadoff DZD.lib
Loading library: ./DZD.lib
Loading: DZD
> complex = loadpdb BCD-DZ1.pdb
Loading PDB file: ./BCD-DZ1.pdb
Enter zPdbReadScan from call depth 0.
Exit zPdbReadScan from call depth 0.
Matching PDB residue names to LEaP variables.
(Residue 0: 4GA, Terminal/beginning, was not found in name map.)
(Residue 1: 4GA, Nonterminal, was not found in name map.)
(Residue 2: 4GA, Nonterminal, was not found in name map.)
(Residue 3: 4GA, Nonterminal, was not found in name map.)
(Residue 4: 4GA, Nonterminal, was not found in name map.)
(Residue 5: 4GA, Nonterminal, was not found in name map.)
(Residue 6: 4GA, Terminal/last, was not found in name map.)
(Residue 7: DZD, Terminal/last, was not found in name map.)
Joining 4GA - 4GA
Joining 4GA - 4GA
Joining 4GA - 4GA
Joining 4GA - 4GA
Joining 4GA - 4GA
Joining 4GA - 4GA
total atoms in file: 176
> bond complex.1.C1 complex.7.O4
> solvateoct complex TIP3PBOX 10 0.78
(using default radius 1.500000 for O4)
(using default radius 1.500000 for O3)
(using default radius 1.500000 for C15)
(using default radius 1.500000 for C14)
(using default radius 1.500000 for C13)
(using default radius 1.500000 for C12)
(using default radius 1.500000 for C11)
(using default radius 1.500000 for C10)
(using default radius 1.500000 for O2)
(using default radius 1.500000 for C9)
(using default radius 1.500000 for C8)
(using default radius 1.500000 for C7)
(using default radius 1.500000 for C6)
(using default radius 1.500000 for C5)
(using default radius 1.500000 for C4)
(using default radius 1.500000 for C3)
(using default radius 1.500000 for C2)
(using default radius 1.500000 for C1)
(using default radius 1.500000 for O1)
Scaling up box by a factor of 1.196399 to meet diagonal cut criterion
Solute vdw bounding box: 16.822 17.335 11.890
Total bounding box for atom centers: 41.263 41.263 41.263
(box expansion for 'iso' is 16.7%)
Solvent unit box: 18.774 18.774 18.774
The number of boxes: x= 3 y= 3 z= 3
Adding box at: x=0 y=0 z=0
Center of solvent box is: 18.774349, 18.774349, 18.774349
Adding box at: x=0 y=0 z=1
Center of solvent box is: 18.774349, 18.774349, 0.000000
Adding box at: x=0 y=0 z=2
Center of solvent box is: 18.774349, 18.774349, -18.774349
Adding box at: x=0 y=1 z=0
Center of solvent box is: 18.774349, 0.000000, 18.774349
Adding box at: x=0 y=1 z=1
Center of solvent box is: 18.774349, 0.000000, 0.000000
Adding box at: x=0 y=1 z=2
Center of solvent box is: 18.774349, 0.000000, -18.774349
Adding box at: x=0 y=2 z=0
Center of solvent box is: 18.774349, -18.774349, 18.774349
Adding box at: x=0 y=2 z=1
Center of solvent box is: 18.774349, -18.774349, 0.000000
Adding box at: x=0 y=2 z=2
Center of solvent box is: 18.774349, -18.774349, -18.774349
Adding box at: x=1 y=0 z=0
Center of solvent box is: 0.000000, 18.774349, 18.774349
Adding box at: x=1 y=0 z=1
Center of solvent box is: 0.000000, 18.774349, 0.000000
Adding box at: x=1 y=0 z=2
Center of solvent box is: 0.000000, 18.774349, -18.774349
Adding box at: x=1 y=1 z=0
Center of solvent box is: 0.000000, 0.000000, 18.774349
Adding box at: x=1 y=1 z=1
Center of solvent box is: 0.000000, 0.000000, 0.000000
Adding box at: x=1 y=1 z=2
Center of solvent box is: 0.000000, 0.000000, -18.774349
Adding box at: x=1 y=2 z=0
Center of solvent box is: 0.000000, -18.774349, 18.774349
Adding box at: x=1 y=2 z=1
Center of solvent box is: 0.000000, -18.774349, 0.000000
Adding box at: x=1 y=2 z=2
Center of solvent box is: 0.000000, -18.774349, -18.774349
Adding box at: x=2 y=0 z=0
Center of solvent box is: -18.774349, 18.774349, 18.774349
Adding box at: x=2 y=0 z=1
Center of solvent box is: -18.774349, 18.774349, 0.000000
Adding box at: x=2 y=0 z=2
Center of solvent box is: -18.774349, 18.774349, -18.774349
Adding box at: x=2 y=1 z=0
Center of solvent box is: -18.774349, 0.000000, 18.774349
Adding box at: x=2 y=1 z=1
Center of solvent box is: -18.774349, 0.000000, 0.000000
Adding box at: x=2 y=1 z=2
Center of solvent box is: -18.774349, 0.000000, -18.774349
Adding box at: x=2 y=2 z=0
Center of solvent box is: -18.774349, -18.774349, 18.774349
Adding box at: x=2 y=2 z=1
Center of solvent box is: -18.774349, -18.774349, 0.000000
Adding box at: x=2 y=2 z=2
Center of solvent box is: -18.774349, -18.774349, -18.774349
(using default radius 1.500000 for O4)
(using default radius 1.500000 for O3)
(using default radius 1.500000 for C15)
(using default radius 1.500000 for C14)
(using default radius 1.500000 for C13)
(using default radius 1.500000 for C12)
(using default radius 1.500000 for C11)
(using default radius 1.500000 for C10)
(using default radius 1.500000 for O2)
(using default radius 1.500000 for C9)
(using default radius 1.500000 for C8)
(using default radius 1.500000 for C7)
(using default radius 1.500000 for C6)
(using default radius 1.500000 for C5)
(using default radius 1.500000 for C4)
(using default radius 1.500000 for C3)
(using default radius 1.500000 for C2)
(using default radius 1.500000 for C1)
(using default radius 1.500000 for O1)
Volume: 37744.518 A^3 (oct)
Mass > 19114.948 amu, Density > 0.841 g/cc
(type - hence mass - of one or more atoms could not be found)
Added 998 residues.
> savepdb complex amber_complex.pdb
Writing pdb file: amber_complex.pdb
> check complex
Checking 'complex'....
Warning: Close contact of 1.470603 angstroms between .R<4GA 7>.A<H3 16> and
.R<DZD 8>.A<H1 20>
Checking parameters for unit 'complex'.
Checking for bond parameters.
Could not find bond parameter for: oh - ho
Could not find bond parameter for: ca - ha
Could not find bond parameter for: ca - ca
Could not find bond parameter for: ca - ha
Could not find bond parameter for: ca - ca
Could not find bond parameter for: ca - oh
Could not find bond parameter for: ca - ca
Could not find bond parameter for: ca - ha
Could not find bond parameter for: ca - ca
Could not find bond parameter for: ca - ha
Could not find bond parameter for: ca - ca
Could not find bond parameter for: ca - ca
Could not find bond parameter for: cd - os
Could not find bond parameter for: cd - h4
Could not find bond parameter for: cc - cd
Could not find bond parameter for: cc - ca
Could not find bond parameter for: c - cc
Could not find bond parameter for: c - o
Could not find bond parameter for: ca - os
Could not find bond parameter for: ca - ca
Could not find bond parameter for: ca - c
Could not find bond parameter for: ca - ca
Could not find bond parameter for: ca - ha
Could not find bond parameter for: ca - ca
Could not find bond parameter for: ca - ha
Could not find bond parameter for: ca - ca
Could not find bond parameter for: ca - ca
Could not find bond parameter for: ca - ca
Could not find bond parameter for: ca - ha
Could not find bond parameter for: oh - ca
Could not find bond parameter for: oh - ho
Checking for angle parameters.
Could not find angle parameter: ca - ca - ha
Could not find angle parameter: ca - ca - oh
Could not find angle parameter: ca - ca - ha
Could not find angle parameter: ca - ca - ha
Could not find angle parameter: ca - ca - ca
Could not find angle parameter: ca - ca - ha
Could not find angle parameter: ca - oh - ho
Could not find angle parameter: ca - ca - ha
Could not find angle parameter: ca - ca - ca
Could not find angle parameter: ca - ca - oh
Could not find angle parameter: ca - ca - ca
Could not find angle parameter: ca - ca - ca
Could not find angle parameter: ca - ca - ha
Could not find angle parameter: ca - ca - ca
Could not find angle parameter: ca - ca - ha
Could not find angle parameter: ca - ca - ca
Could not find angle parameter: ca - ca - ha
Could not find angle parameter: os - cd - h4
Could not find angle parameter: cd - cc - ca
Could not find angle parameter: cc - c - o
Could not find angle parameter: cc - cd - os
Could not find angle parameter: cc - cd - h4
Could not find angle parameter: cc - ca - ca
Could not find angle parameter: cc - ca - ca
Could not find angle parameter: c - cc - cd
Could not find angle parameter: c - cc - ca
Could not find angle parameter: ca - ca - ha
Could not find angle parameter: ca - ca - c
Could not find angle parameter: ca - os - cd
Could not find angle parameter: ca - ca - ha
Could not find angle parameter: ca - ca - os
Could not find angle parameter: ca - c - cc
Could not find angle parameter: ca - c - o
Could not find angle parameter: ca - ca - ha
Could not find angle parameter: ca - ca - ca
Could not find angle parameter: ca - ca - c
Could not find angle parameter: ca - ca - ca
Could not find angle parameter: ca - ca - ha
Could not find angle parameter: ca - oh - ho
Could not find angle parameter: ca - ca - ca
Could not find angle parameter: ca - ca - ha
Could not find angle parameter: ca - ca - ca
Could not find angle parameter: ca - ca - ha
Could not find angle parameter: ca - ca - ca
Could not find angle parameter: ca - ca - ca
Could not find angle parameter: ca - ca - os
Could not find angle parameter: oh - ca - ca
Could not find angle parameter: oh - ca - ca
There are missing parameters.
check: Warnings: 1
Unit is OK.
> saveamberparm complex prmtop.complex inpcrd.complex
Checking Unit.
Building topology.
Building atom parameters.
For atom: .R<DZD 8>.A<O1 1> Could not find vdW (or other) parameters for
type: oh
For atom: .R<DZD 8>.A<C1 2> Could not find vdW (or other) parameters for
type: ca
For atom: .R<DZD 8>.A<C2 3> Could not find vdW (or other) parameters for
type: ca
For atom: .R<DZD 8>.A<C3 4> Could not find vdW (or other) parameters for
type: ca
For atom: .R<DZD 8>.A<C4 5> Could not find vdW (or other) parameters for
type: ca
For atom: .R<DZD 8>.A<C5 6> Could not find vdW (or other) parameters for
type: ca
For atom: .R<DZD 8>.A<C6 7> Could not find vdW (or other) parameters for
type: ca
For atom: .R<DZD 8>.A<C7 8> Could not find vdW (or other) parameters for
type: c
For atom: .R<DZD 8>.A<C8 9> Could not find vdW (or other) parameters for
type: cc
For atom: .R<DZD 8>.A<C9 10> Could not find vdW (or other) parameters for
type: cd
For atom: .R<DZD 8>.A<O2 11> Could not find vdW (or other) parameters for
type: os
For atom: .R<DZD 8>.A<C10 12> Could not find vdW (or other) parameters for
type: ca
For atom: .R<DZD 8>.A<C11 13> Could not find vdW (or other) parameters for
type: ca
For atom: .R<DZD 8>.A<C12 14> Could not find vdW (or other) parameters for
type: ca
For atom: .R<DZD 8>.A<C13 15> Could not find vdW (or other) parameters for
type: ca
For atom: .R<DZD 8>.A<C14 16> Could not find vdW (or other) parameters for
type: ca
For atom: .R<DZD 8>.A<C15 17> Could not find vdW (or other) parameters for
type: ca
For atom: .R<DZD 8>.A<O3 18> Could not find vdW (or other) parameters for
type: o
For atom: .R<DZD 8>.A<O4 19> Could not find vdW (or other) parameters for
type: oh
For atom: .R<DZD 8>.A<H1 20> Could not find vdW (or other) parameters for
type: ha
For atom: .R<DZD 8>.A<H2 21> Could not find vdW (or other) parameters for
type: ha
For atom: .R<DZD 8>.A<H3 22> Could not find vdW (or other) parameters for
type: ha
For atom: .R<DZD 8>.A<H4 23> Could not find vdW (or other) parameters for
type: ha
For atom: .R<DZD 8>.A<H5 24> Could not find vdW (or other) parameters for
type: ha
For atom: .R<DZD 8>.A<H6 25> Could not find vdW (or other) parameters for
type: ha
For atom: .R<DZD 8>.A<H7 26> Could not find vdW (or other) parameters for
type: ha
For atom: .R<DZD 8>.A<H8 27> Could not find vdW (or other) parameters for
type: ho
For atom: .R<DZD 8>.A<H9 28> Could not find vdW (or other) parameters for
type: h4
For atom: .R<DZD 8>.A<H10 29> Could not find vdW (or other) parameters for
type: ho
Parameter file was not saved.
> quit
Quit
regards, Fateme
--
Fatemeh sadat Fateminasab
PhD candidate of physical chemistry
Isfahan university
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Received on Tue Jan 24 2017 - 04:00:02 PST
