Dear Amber users,
I am using AMBER 14 for Md simulations of amino acids and pure ionic liquids (without water) by generating the resp charges and producing the library files for all all amino acids and ionic liquid ions. The simulations have been successful using single forcefield i.e. GAFF. Now the problem,
I want to add water to my systems( i have done it using packmol), run the simulations again and for water i have to use ff14SB and parameters from some water model(e.g frcmod.ionsjc_tip4pew). But when i use the following input file for tleap to generate the topology and prmtop files i get the error.
Input file:
source leaprc.gaff
source leaprc.ff14SB
loadamberparams frcmod.ionsjc_tip4pew
loadoff ACT.lib (acetate ion lib)
loadoff EMI.lib (EMIM cation lib)
loadoff LYS-scaled.lib (non-standard LYS charged)
loadamberparams emim.frcmod
loadamberparams acetate.frcmod
loadamberparams lys-charged.frcmod
box= loadpdb box-lys.pdb
setbox box centers
saveamberparm box box-lys.prmtop box-lys.inpcrd
generating prmtop and inpcrd file error by leap
Loading PDB file: ./box-lys-WATER.pdb
(starting new molecule for chain B)
(starting new molecule for chain C)
(starting new molecule for chain D)
Created a new atom named: C1 within residue: .R<NLYS 441>
Created a new atom named: N1 within residue: .R<NLYS 441>
Created a new atom named: C2 within residue: .R<NLYS 441>
. . . . . . . . .
. . . . . . . . .
Created a new atom named: H13 within residue: .R<NLYS 441>
Created a new atom named: H14 within residue: .R<NLYS 441>
Created a new atom named: H15 within residue: .R<NLYS 441>
Added missing heavy atom: .R<NLYS 441>.A<N 1>
Added missing heavy atom: .R<NLYS 441>.A<CA 5>
Added missing heavy atom: .R<NLYS 441>.A<CB 7>
Added missing heavy atom: .R<NLYS 441>.A<C 23>
Added missing heavy atom: .R<NLYS 441>.A<CG 10>
Added missing heavy atom: .R<NLYS 441>.A<O 24>
Added missing heavy atom: .R<NLYS 441>.A<CD 13>
Added missing heavy atom: .R<NLYS 441>.A<CE 16>
Added missing heavy atom: .R<NLYS 441>.A<NZ 19>
One sided connection. Residue: LYS missing connect0 atom.
One sided connection. Residue: default_name missing connect1 atom.
Created a new atom named: C1 within residue: .R<CLYS 480>
Created a new atom named: N1 within residue: .R<CLYS 480>
Created a new atom named: H1 within residue: .R<CLYS 480>
. . . . . . . . .
. . . . . . . . .
Created a new atom named: H13 within residue: .R<CLYS 480>
Created a new atom named: H14 within residue: .R<CLYS 480>
Created a new atom named: H15 within residue: .R<CLYS 480>
Added missing heavy atom: .R<CLYS 480>.A<OXT 23>
Added missing heavy atom: .R<CLYS 480>.A<C 21>
. . . . . . . . .
. . . . . . . . .
Added missing heavy atom: .R<CLYS 480>.A<CE 14>
Added missing heavy atom: .R<CLYS 480>.A<NZ 17>
total atoms in file: 8880
Leap added 44 missing atoms according to residue templates:
19 Heavy
25 H / lone pairs
The file contained 47 atoms not in residue templates
Box dimensions: 63.295869 61.074908 64.409618
Checking Unit.
ERROR: The unperturbed charge of the unit: 0.400270 is not integral.
WARNING: The unperturbed charge of the unit: 0.400270 is not zero.
FATAL: Atom .R<NLYS 441>.A<C1 25> does not have a type.
FATAL: Atom .R<NLYS 441>.A<N1 26> does not have a type.
. . . . . . . . .
. . . . . . . . .
FATAL: Atom .R<CLYS 480>.A<H13 46> does not have a type.
FATAL: Atom .R<CLYS 480>.A<H14 47> does not have a type.
FATAL: Atom .R<CLYS 480>.A<H15 48> does not have a type.
Failed to generate parameters
Parameter file was not saved.
leap creates new atoms within 2 out of 40 LYS residues in the pdb file i.e. No.1 (441) LYS and No.40 (480)LYS in the PDB file. Can anybody suggest how it should be dealt with as i dont want leap to read any of my LYS as CLYS or NLYS?
Regards,
Shafaq
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Received on Tue May 23 2017 - 06:00:03 PDT
