Dear David,
I used
source leaprc.ff99SB
source leaprc.gaff
*LIG *= loadmol2 lig_h.mol2
list
check *LIG *
loadamberparams lig_h.frcmod
saveoff *LIG *lig_h.lib
saveamberparm *LIG *lig_h.prmtop lig_h.inpcrd
savepdb *LIG *lig_f.pdb
quit
instead of
source leaprc.ff99SB
source leaprc.gaff
*lig*= loadmol2 lig_h.mol2
list
check *lig*
loadamberparams lig_h.frcmod
saveoff *lig *lig_h.lib
saveamberparm *lig *lig_h.prmtop lig_h.inpcrd
savepdb *lig* lig_f.pdb
quit
----------------------------------------------------------------------------
Then, I loaded pdb file of protein-ligand compex:
Added missing heavy atom: .R<CASP 545>.A<OXT 13>
Added missing heavy atom: .R<LIG 546>.A<C20 24>
Added missing heavy atom: .R<LIG 546>.A<C19 23>
Added missing heavy atom: .R<LIG 546>.A<C21 25>
Added missing heavy atom: .R<LIG 546>.A<C18 22>
Added missing heavy atom: .R<LIG 546>.A<C16 20>
Added missing heavy atom: .R<LIG 546>.A<C17 21>
Added missing heavy atom: .R<LIG 546>.A<C15 19>
Added missing heavy atom: .R<LIG 546>.A<N2 3>
Added missing heavy atom: .R<LIG 546>.A<O3 29>
Added missing heavy atom: .R<LIG 546>.A<N1 2>
Added missing heavy atom: .R<LIG 546>.A<C14 18>
Added missing heavy atom: .R<LIG 546>.A<C11 15>
Added missing heavy atom: .R<LIG 546>.A<C10 14>
Added missing heavy atom: .R<LIG 546>.A<C12 16>
Added missing heavy atom: .R<LIG 546>.A<C9 13>
Added missing heavy atom: .R<LIG 546>.A<C7 11>
Added missing heavy atom: .R<LIG 546>.A<C13 17>
Added missing heavy atom: .R<LIG 546>.A<C8 12>
Added missing heavy atom: .R<LIG 546>.A<C6 10>
Added missing heavy atom: .R<LIG 546>.A<O1 27>
Added missing heavy atom: .R<LIG 546>.A<O2 28>
Added missing heavy atom: .R<LIG 546>.A<C5 9>
Added missing heavy atom: .R<LIG 546>.A<C4 8>
Added missing heavy atom: .R<LIG 546>.A<C3 7>
Added missing heavy atom: .R<LIG 546>.A<C2 6>
Added missing heavy atom: .R<LIG 546>.A<C1 5>
total atoms in file: 5029
Leap added 40 missing atoms according to residue templates:
27 Heavy
13 H / lone pairs
---------------------------------------------------------------------------------------------------------------
> saveamberparm comp comp.prmtop comp.inpcrd
Checking Unit.
WARNING: There is a bond of 3.540892 angstroms between:
------- .R<LIG 546>.A<C21 25> and .R<LIG 546>.A<H01 32>
WARNING: There is a bond of 4.314909 angstroms between:
------- .R<LIG 546>.A<C19 23> and .R<LIG 546>.A<H12 43>
WARNING: There is a bond of 7.015901 angstroms between:
------- .R<LIG 546>.A<C18 22> and .R<LIG 546>.A<H11 42>
WARNING: There is a bond of 7.853752 angstroms between:
------- .R<LIG 546>.A<C17 21> and .R<LIG 546>.A<H10 41>
WARNING: There is a bond of 3.441098 angstroms between:
------- .R<LIG 546>.A<C10 14> and .R<LIG 546>.A<H08 39>
WARNING: There is a bond of 6.403408 angstroms between:
------- .R<LIG 546>.A<C9 13> and .R<LIG 546>.A<H07 38>
WARNING: There is a bond of 6.985666 angstroms between:
------- .R<LIG 546>.A<C8 12> and .R<LIG 546>.A<H06 37>
WARNING: There is a bond of 10.048551 angstroms between:
------- .R<LIG 546>.A<C6 10> and .R<LIG 546>.A<O 26>
WARNING: There is a bond of 6.073154 angstroms between:
------- .R<LIG 546>.A<C5 9> and .R<LIG 546>.A<H05 36>
WARNING: There is a bond of 7.130917 angstroms between:
------- .R<LIG 546>.A<C4 8> and .R<LIG 546>.A<H04 35>
WARNING: There is a bond of 8.035942 angstroms between:
------- .R<LIG 546>.A<C2 6> and .R<LIG 546>.A<H03 34>
WARNING: There is a bond of 6.746334 angstroms between:
------- .R<LIG 546>.A<C1 5> and .R<LIG 546>.A<H02 33>
WARNING: There is a bond of 7.962667 angstroms between:
------- .R<LIG 546>.A<C 4> and .R<LIG 546>.A<C14 18>
WARNING: There is a bond of 3.264369 angstroms between:
------- .R<LIG 546>.A<N 1> and .R<LIG 546>.A<C3 7>
WARNING: There is a bond of 10.821147 angstroms between:
------- .R<LIG 546>.A<N 1> and .R<LIG 546>.A<C6 10>
WARNING: There is a bond of 12.593285 angstroms between:
------- .R<LIG 546>.A<N 1> and .R<LIG 546>.A<H 30>
WARNING: The unperturbed charge of the unit: -8.000000 is not zero.
-- ignoring the warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 1060 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
CASP 1
LIG 1
NCYS 1
)
(no restraints)
The comp.prmtop and comp.inpcrd files were created. But I encountered with
many warning.
savepdb comp comp_f.pdb
When I saw comp_f.pdb using vmd, there was unusual ligand.
Please find the figure in following link:
https://www.dropbox.com/s/kkdhuypwltchpti/ligand.png?dl=0
How to resolve this problem?
Best,
Atila
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Received on Fri Sep 18 2015 - 04:30:03 PDT
