the pdb file you provided for the ligand has the same problem - atoms are
very far apart.
you'll need to focus on how you generated the ligand structure and fix that
before running leap.
On Fri, Dec 11, 2015 at 10:30 AM, Andrew Bostick <andrew.bostick1.gmail.com>
wrote:
> Dear amber users
>
> I am creating prmtop and inpcrd files for my ligand.
>
> For ligand only, my manner is as follows (all things is ok):
>
> $AMBERHOME/bin/antechamber -i lig_h.pdb -fi pdb -o lig_h.mol2 -fo mol2 -c
> bcc -s 2
>
> $AMBERHOME/bin/parmchk -i lig_h.mol2 -f mol2 -o lig_h.frcmod
>
> tleap -f tleap_lig.in
>
> The tleap_lig.in file is as follows:
> ---------------------------------------------------------------
> source leaprc.ff99SB
>
> source leaprc.gaff
>
> LIG = loadmol2 lig_h.mol2
>
> list
>
> check LIG
>
> loadamberparams lig_h.frcmod
>
> saveoff LIG lig_h.lib
>
> set default PBRadii mbondi2
>
> saveamberparm LIG lig_h.prmtop lig_h.inpcrd
>
> savepdb LIG lig_f.pdb
>
> quit
> ---------------------------------------------------------------
>
> For protein-ligand complex, I used:
>
> source leaprc.ff99SB
>
> source leaprc.gaff
>
> loadamberparams lig_h.frcmod
>
> loadoff lig_h.lib
>
> comp = loadpdb comp.pdb
>
> set default PBRadii mbondi2
>
> saveamberparm comp comp.prmtop comp.inpcrd
>
> savepdb comp comp_f.pdb
>
> quit
> ---------------------------------------------------------------
>
> But I encountered with warning about ligand atoms:
>
> > saveamberparm comp comp.prmtop comp.inpcrd
> Checking Unit.
> WARNING: There is a bond of 420.000806 angstroms between:
> ------- .R<LIG 546>.A<O2 28> and .R<LIG 546>.A<H2 31>
> WARNING: There is a bond of 140.000816 angstroms between:
> ------- .R<LIG 546>.A<C21 25> and .R<LIG 546>.A<H01 32>
> WARNING: There is a bond of 150.002038 angstroms between:
> ------- .R<LIG 546>.A<C20 24> and .R<LIG 546>.A<C21 25>
> WARNING: There is a bond of 610.000968 angstroms between:
> ------- .R<LIG 546>.A<C20 24> and .R<LIG 546>.A<H13 44>
> WARNING: There is a bond of 660.000281 angstroms between:
> ------- .R<LIG 546>.A<C19 23> and .R<LIG 546>.A<C20 24>
> WARNING: There is a bond of 390.000480 angstroms between:
> ------- .R<LIG 546>.A<C19 23> and .R<LIG 546>.A<H12 43>
> WARNING: There is a bond of 540.001784 angstroms between:
> ------- .R<LIG 546>.A<C18 22> and .R<LIG 546>.A<C19 23>
> WARNING: There is a bond of 10.011275 angstroms between:
> ------- .R<LIG 546>.A<C18 22> and .R<LIG 546>.A<H11 42>
> WARNING: There is a bond of 210.001449 angstroms between:
> ------- .R<LIG 546>.A<C17 21> and .R<LIG 546>.A<C18 22>
> WARNING: There is a bond of 360.001638 angstroms between:
> ------- .R<LIG 546>.A<C17 21> and .R<LIG 546>.A<H10 41>
> WARNING: There is a bond of 270.000660 angstroms between:
> ------- .R<LIG 546>.A<C16 20> and .R<LIG 546>.A<C17 21>
> WARNING: There is a bond of 330.002961 angstroms between:
> ------- .R<LIG 546>.A<C16 20> and .R<LIG 546>.A<C21 25>
> WARNING: There is a bond of 470.000700 angstroms between:
> ------- .R<LIG 546>.A<C15 19> and .R<LIG 546>.A<C16 20>
> WARNING: There is a bond of 30.025041 angstroms between:
> ------- .R<LIG 546>.A<C15 19> and .R<LIG 546>.A<O3 29>
> WARNING: There is a bond of 460.000272 angstroms between:
> ------- .R<LIG 546>.A<C14 18> and .R<LIG 546>.A<O3 29>
> WARNING: There is a bond of 200.000210 angstroms between:
> ------- .R<LIG 546>.A<C13 17> and .R<LIG 546>.A<O1 27>
> WARNING: There is a bond of 100.000828 angstroms between:
> ------- .R<LIG 546>.A<C13 17> and .R<LIG 546>.A<O2 28>
> WARNING: There is a bond of 550.000699 angstroms between:
> ------- .R<LIG 546>.A<C12 16> and .R<LIG 546>.A<C13 17>
> WARNING: There is a bond of 440.002158 angstroms between:
> ------- .R<LIG 546>.A<C11 15> and .R<LIG 546>.A<C12 16>
> WARNING: There is a bond of 150.000430 angstroms between:
> ------- .R<LIG 546>.A<C11 15> and .R<LIG 546>.A<H09 40>
> WARNING: There is a bond of 330.001263 angstroms between:
> ------- .R<LIG 546>.A<C10 14> and .R<LIG 546>.A<C11 15>
> WARNING: There is a bond of 40.014043 angstroms between:
> ------- .R<LIG 546>.A<C10 14> and .R<LIG 546>.A<H08 39>
> WARNING: There is a bond of 260.000383 angstroms between:
> ------- .R<LIG 546>.A<C9 13> and .R<LIG 546>.A<C10 14>
> WARNING: There is a bond of 100.002492 angstroms between:
> ------- .R<LIG 546>.A<C9 13> and .R<LIG 546>.A<H07 38>
> WARNING: There is a bond of 420.002195 angstroms between:
> ------- .R<LIG 546>.A<C8 12> and .R<LIG 546>.A<C9 13>
> WARNING: There is a bond of 160.000370 angstroms between:
> ------- .R<LIG 546>.A<C8 12> and .R<LIG 546>.A<H06 37>
> WARNING: There is a bond of 380.001178 angstroms between:
> ------- .R<LIG 546>.A<C7 11> and .R<LIG 546>.A<C8 12>
> WARNING: There is a bond of 330.000319 angstroms between:
> ------- .R<LIG 546>.A<C7 11> and .R<LIG 546>.A<C12 16>
> WARNING: There is a bond of 330.002902 angstroms between:
> ------- .R<LIG 546>.A<C6 10> and .R<LIG 546>.A<C7 11>
> WARNING: There is a bond of 520.000250 angstroms between:
> ------- .R<LIG 546>.A<C6 10> and .R<LIG 546>.A<O 26>
> WARNING: There is a bond of 880.000010 angstroms between:
> ------- .R<LIG 546>.A<C5 9> and .R<LIG 546>.A<H05 36>
> WARNING: There is a bond of 250.003339 angstroms between:
> ------- .R<LIG 546>.A<C4 8> and .R<LIG 546>.A<C5 9>
> WARNING: There is a bond of 40.009330 angstroms between:
> ------- .R<LIG 546>.A<C4 8> and .R<LIG 546>.A<H04 35>
> WARNING: There is a bond of 20.000846 angstroms between:
> ------- .R<LIG 546>.A<C3 7> and .R<LIG 546>.A<C4 8>
> WARNING: There is a bond of 620.001013 angstroms between:
> ------- .R<LIG 546>.A<C2 6> and .R<LIG 546>.A<C3 7>
> WARNING: There is a bond of 790.000011 angstroms between:
> ------- .R<LIG 546>.A<C2 6> and .R<LIG 546>.A<H03 34>
> WARNING: There is a bond of 260.003180 angstroms between:
> ------- .R<LIG 546>.A<C1 5> and .R<LIG 546>.A<C2 6>
> WARNING: There is a bond of 60.006192 angstroms between:
> ------- .R<LIG 546>.A<C1 5> and .R<LIG 546>.A<H02 33>
> WARNING: There is a bond of 30.000602 angstroms between:
> ------- .R<LIG 546>.A<C 4> and .R<LIG 546>.A<C1 5>
> WARNING: There is a bond of 620.001013 angstroms between:
> ------- .R<LIG 546>.A<C 4> and .R<LIG 546>.A<C5 9>
> WARNING: There is a bond of 150.006057 angstroms between:
> ------- .R<LIG 546>.A<C 4> and .R<LIG 546>.A<C14 18>
> WARNING: There is a bond of 850.000034 angstroms between:
> ------- .R<LIG 546>.A<N2 3> and .R<LIG 546>.A<C15 19>
> WARNING: There is a bond of 450.001436 angstroms between:
> ------- .R<LIG 546>.A<N1 2> and .R<LIG 546>.A<N2 3>
> WARNING: There is a bond of 90.003818 angstroms between:
> ------- .R<LIG 546>.A<N1 2> and .R<LIG 546>.A<C14 18>
> WARNING: There is a bond of 290.003027 angstroms between:
> ------- .R<LIG 546>.A<N 1> and .R<LIG 546>.A<C3 7>
> WARNING: There is a bond of 220.000899 angstroms between:
> ------- .R<LIG 546>.A<N 1> and .R<LIG 546>.A<C6 10>
> WARNING: There is a bond of 910.000154 angstroms between:
> ------- .R<LIG 546>.A<N 1> and .R<LIG 546>.A<H 30>
> WARNING: The unperturbed charge of the unit: -7.999000 is not zero.
>
> -- ignoring the warnings.
>
>
> -------------------------------------------------------------------------------------------------------------
>
> Please check my pdb, mol2 and lib files for ligand in following links:
>
> https://www.dropbox.com/s/vovx08lsk7oi6w2/lig_h.pdb?dl=0
>
> https://www.dropbox.com/s/por0ma0v281z1zk/lig_h.mol2?dl=0
>
> https://www.dropbox.com/s/vo38bnxlvu4m6m6/lig_h.lib?dl=0
>
> How to resolve this issue?
>
> Any help will highly appreciated.
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>
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Received on Fri Dec 11 2015 - 08:00:06 PST
