Kedar Potdar wrote:
Hi friends,
I have compiled Gromacs on native windows. The first two program in demo
script (perl implementation of script “demo”) work fine but genbox
displays following output
Reading solute configuration
Glycine aRginine prOline Methionine Alanine Cystine Serine
Containing 145 atoms in 13 residues
Initialising van der waals distances...
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 2x2x2 boxes
Generating configuration
Sorting configuration
Found 1 molecule type:
SOL ( 3 atoms): 1728 residues
Calculating Overlap...
box_margin = 0.315
Removed 2895 atoms that were outside the box
Succesfully made neighbourlist
nri = 11448, nrj = 456822
Checking Protein-Solvent overlap: tested 4131 pairs, removed 228 atoms.
Checking Solvent-Solvent overlap: tested 36954 pairs, removed 597 atoms.
Added 488 molecules
Generated solvent containing 1464 atoms in 488 residues
Writing generated configuration to cpeptide_b4em.gro
Glycine aRginine prOline Methionine Alanine Cystine Serine
Output configuration contains 1609 atoms in 501 residues
Volume : 17.1176 (nm^3)
Density : 1002.99 (g/l)
Number of SOL molecules: 488
Processing topology
Back Off! I just backed up cpeptide.top to ./#cpeptide.top.1#
*Cpeptide.top file is of zero bytes now… and all further programs in the
test fail after this.*
* *
Has anybody faced such problem before? What is remedy for this problem?
Check the source code for opening of the file in genbox. It tries to
append to the file, and the code for that may be different windows than
under Unix.
--
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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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