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

[David van der Spoel]

Shanjie Huang wrote:
> 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

You are trying to build a box of 1 micrometer cubed.

> 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


-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++