Re: [AMBER] segmentation_fault_loading_pdb in tleap

From: Soumendranath Bhakat <>
Date: Sat, 21 Jun 2014 15:34:50 +0200

Update your AmberTools. Before uploading any receptor prepare it using MMV
or Glide. To solve this open your rec.pdb with MMV, which will
automatically correct your receptor. After saving it in .pdb format; open
it again with Chimera and delete all hydrogens and save it as rec.pdb

try this tleap file. I presume you are running a typical ligand and
receptor complex. Update AmberTools i

source leaprc.ff99SB
source leaprc.gaff
LIG = loadmol2 LIG.mol2
loadamberparams LIG.frcmod
check LIG
receptor = loadPDB rec.pdb
complex = combine {receptor LIG}
set default PBRadii mbondi2
saveAmberParm LIG LIG.crd
receptor = loadPDB rec.pdb
saveAmberParm receptor rec.crd
saveAmberParm complex com.crd
savepdb complex complex_gas.pdb
charge complex
addIons2 complex Na+ 0
solvateBox complex TIP3PBOX 8.0
saveAmberParm complex com_solvated.crd
savepdb complex com_solvated.pdb


On Sat, Jun 21, 2014 at 2:56 PM, Shomesankar Bhunia <> wrote:

> Dear all,
> I am having a problem while setting a system for MD simulation in amber.
> I am having a ligand bound at the interface of two protein structures. I am
> using reduce to trim the the hydrogens and applying tleap to add hydrogens.
> I am getting segmentation fault while loading the protein ligand
> complex.The command line is
> ./tleap -f leaprc.ff99SBildn
> >source leaprc.gaff
> >loadamberparams lig_m.frcmod
> Loading parameters: ./azixa_lig_m.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> remark goes here
> >loadoff lig_m.lib
> Loading library: ./azixa_lig_m.lib
> >complex = loadpdb lig_prot_noh.pdb
> Loading PDB file: ./azixa_lig_prot_noh.pdb
> Added missing heavy atom: .R<CGLY 436>.A<OXT 8>
> Added missing heavy atom: .R<CASP 853>.A<OXT 13>
> Segmentation fault (core dumped)
> The GLY 436 and ASP 853 are the terminal residues of the two protein
> structures respectively. How to overcome the problem? Thanks in advance.
> _______________________________________________
> AMBER mailing list

Thanks & Regards;
Soumendranath Bhakat
AMBER mailing list
Received on Sat Jun 21 2014 - 07:00:02 PDT
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