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
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jun 21 2014 - 06:00:03 PDT
