[AMBER] segmentation_fault_loading_pdb in tleap

From: Shomesankar Bhunia <rightclickatrighttime.gmail.com>
Date: Sat, 21 Jun 2014 18:26:11 +0530

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.
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Received on Sat Jun 21 2014 - 06:00:03 PDT
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