[gmx-users] genbox fatal error with ligand-receptor complex: realloc for atoms_solvt->atomname : No such file or directory

[Shanjie Huang]

Hi,
I am working on a molecular dynamics of a receptor-ligand complex. I
created the .gro files for receptor and ligand separatedly and merged
them together, making sure the atom numbers are continuous. In the .top
file of receptor I have put " #include "ligand.itp" " and append a line
for ligand in [molecule section]. Then I executed "editconf"
successfully. When I execute:
genbox -cp receptor.gro -cs spc216.gro -o receptor_1.gro -p receptor.top

Error occured:
---------------------------------------
Reading solute configuration
CERM PROTESE
Containing 982 atoms in 100 residues
Initialising van der waals distances...
Opening library file /gdata/gromacs/share/top/vdwradii.dat
Opening library file /gdata/gromacs/share/top/aminoacids.dat
Reading solvent configuration
"216H2O,WATJP01,SPC216,SPC-MODEL,300K,BOX(M)=1.86206NM,WFVG,MAR. 1984"
solvent configuration contains 648 atoms in 216 residues

Initialising van der waals distances...
Will generate new solvent configuration of 516x487x422 boxes
Fatal error: realloc for atoms_solvt->atomname (-8686336 bytes, file
genbox.c, line 390, atoms_solvt->atomname=0x0x101bbs98): No such file or
directory
--------------------------------------------------------
What should I do then? Please give me a hand. Thanks.

Sincerely
MC Yan
-- 
  Shanjie Huang
  suibingkuai at 123mail.org

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