Hi Elvis
The only PDB file is my protein and I already checked the file.
I used the same previous steps with the same protein and another ligand and
this error didn't happen.
Em seg., 29 de jun. de 2020 às 10:06, Elvis Martis <elvis_bcp.elvismartis.in>
escreveu:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Prof Dr Renato Costa
Instituto Federal do Pará - IFPA
Grupo de Modelagem Molecular - UFPA
Tel.+55 91 985484622
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jun 29 2020 - 06:30:06 PDT
