Hi
One of your PDB files still has some conect entries. You must delete them
before loading in to leap.
Best Regards
Elvis
On Mon, 29 Jun 2020 at 18:20, Renato Araujo <renatoacufpa.gmail.com> wrote:
> Hello everyone
> I'm trying to build a protein-ligand system. The input is broken down here.
> source leaprc.protein.ff14SB
> source leaprc.gaff2
> source leaprc.water.tip3p
> loadamberparams frcmod.ionsjc_tip3p
> set default PBRadii mbondi2
> loadamberparams LIG_resp.frcmod
> lig = loadmol2 LIG_resp.mol2
> rec = loadpdb pro.pdb
> com = combine {rec lig}
> savepdb lig ligand.pdb
> saveamberparm lig ligand.prmtop ligand.inpcrd
> savepdb rec receptor.pdb
> saveamberparm rec receptor.prmtop receptor.inpcrd
> savepdb com complex.pdb
> saveamberparm com complex.prmtop complex.inpcrd
> charge com
> addions com Na+ 0.0
> charge com
> solvateoct com TIP3PBOX 12.0
> savepdb com complex_solv.pdb
> saveamberparm com complex_solv.prmtop complex_solv.inpcrd
> quit
>
> Then I get the following error
>
> Loading parameters: ./LIG_resp.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> Remark line goes here
> Loading Mol2 file: ./LIG_resp.mol2
> Reading MOLECULE named UNK
> Loading PDB file: ./pro.pdb
> total atoms in file: 4683
> Writing pdb file: ligand.pdb
> Checking Unit.
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Building angle parameters.
> Building proper torsion parameters.
> !FATAL ERROR----------------------------------------
> !FATAL: In file [unitio.c], line 1810
> !FATAL: Message: 1-4: cannot add bond 1 2
> This may be caused by duplicate bond specifications;
> for example, explicit bond commands in addition to PDB conect records.
> !
> !ABORTING.
>
> how to fix this error?
>
> NOTE: I set up two other systems with different ligand with the same
> protein and did not present an error.
>
> --
> Prof Dr Renato Costa
> Instituto Federal do Pará - IFPA
> Grupo de Modelagem Molecular - UFPA
> Tel.+55 91 985484622
> _______________________________________________
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>
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Received on Mon Jun 29 2020 - 06:30:04 PDT
