[AMBER] error message create parameters

From: Renato Araujo <renatoacufpa.gmail.com>
Date: Mon, 29 Jun 2020 09:49:42 -0300

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

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.

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 ParĂ¡ - IFPA
Grupo de Modelagem Molecular - UFPA
Tel.+55  91 985484622
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Received on Mon Jun 29 2020 - 06:00:09 PDT
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