Yeah actually I got cause of the problem... :) I need to remove the "topinput" file before renaming "TEMP_FILENM" with " topinput".
Thanks... -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Tuesday, May 29, 2007 6:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Genbox problem ... 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 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
