Fatal Error Chdir Failed Namd
Kohlmeyer: "Re: psfgen: more problem" Reply: Axel Kohlmeyer: "Re: psfgen: more problem" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] As i wrote in earlier mail, the problem is also happenning for DNA molecules as well> the 1LAE structure is also giving the error like $ vmd -dispdev text -e cku.pgn Info) VMD for LINUX, version 1.8.6 (April 6, 2007) Info) http://www.ks.uiuc.edu/Research/vmd/ Info) Email questions and bug reports to vmd_at_ks.uiuc.edu Info) Please include this reference in published work using VMD: Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38. Info) ------------------------------------------------------------- Info) Multithreading available, 2 CPUs detected. Info) Free system memory: 2114MB (69%) 1.4.5 reading topology file top_all27_na.rtf \\\\ CHARMM27 All-Hydrogen Nucleic Acid Topology File //// \\\\\\\\\\\\\\\\\\ Developmental //////////////////////// Alexander D. MacKerell Jr. and Nicolas Foloppe December, 2003 All comments to ADM jr. via the CHARMM web site: www.charmm.org parameter set discussion forum Created by CHARMM version 27 1 aliasing residue A to ADE aliasing residue C to CYT aliasing residue T to THY aliasing residue G to GUA building segment U reading residues from pdb file la.pdb unknown residue type C A extracted 1 residues from pdb file Info: generating structure.... unknown residue type C A ERROR: failed on end of segment MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over. MOLECULE MISSING! Use resetpsf to start over. MOLECULE MISSING! Use resetpsf to start over. MOLECULE MISSING! Use resetpsf to start over. MOLECULE MISSING! Use resetpsf to start over. my pgn file is : package require psfgen topology top_all27_na.rtf pdbalias residue A ADE pdbalias residue C CYT pdbalias residue T THY pdbalias residue G GUA #pdbalias atom ILE CD1 CD segment U
water from a .dcd file or .coor file" Next in thread: DimitryASuplatov: "Re: Installation of NAMD & charm - fatal errors" Reply: DimitryASuplatov: "Re: Installation of NAMD & charm - fatal errors" Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ] Hi, Struggling to get NAMD working. I have downloaded NAMD 2.7b2 for http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2008-2009/1103.html Linux-x86_64 and the Charm++ source codes. Worked my way through the following from the notes/readmes: [quote] npack NAMD and matching Charm++ source code and enter directory: tar xzf NAMD_2.7b2_Source.tar.gz cd NAMD_2.7b2_Source tar xf charm-6.1.3.tar cd charm-6.1.3 Build and test the Charm++/Converse library: ./build charm++ net-linux-x86_64 --no-build-shared -O -DCMK_OPTIMIZE=1 http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2010-2011/0485.html cd net-linux-x86_64/tests/charm++/megatest make pgm ./charmrun ++local +p4 ./pgm (also try running on multiple nodes) cd ../../../../.. Download and install TCL and FFTW libraries: (cd to NAMD_2.7b2_Source if you're not already there) wget http://www.ks.uiuc.edu/Research/namd/libraries/fftw-linux-x86_64.tar.gz tar xzf fftw-linux-x86_64.tar.gz mv linux-x86_64 fftw wget http://www.ks.uiuc.edu/Research/namd/libraries/tcl-linux-x86_64.tar.gz tar xzf tcl-linux-x86_64.tar.gz mv linux-x86_64 tcl [/quote] However, ./namd2 or ./namd2 src/alanin throw up fatal errors ("No simulation config file specified on command line" and "chdir() failed!" respectively). Can anyone help please?? I note that I could not find any files associated with the following section in the readme file: [quote] Optionally edit various configuration files: (not needed if charm-6.1.3, fftw, and tcl are in NAMD_2.7b2_Source) vi Make.charm (set CHARMBASE to full path to charm) vi arch/Linux-x86_64.fftw (fix library name and path to files) vi arch/Linux-x86_64.tcl (fix library version and path to TCL files) Sllet up build directory and compile: ./con
here for a quick overview of the site Help Center Detailed answers to any questions you might have Meta Discuss the workings and policies of this site About Us Learn more about Stack Overflow the company http://stackoverflow.com/questions/20105260/what-does-stale-file-handle-in-linux-means Business Learn more about hiring developers or posting ads with us Stack Overflow Questions Jobs Documentation Tags Users Badges Ask Question x Dismiss Join the Stack Overflow Community Stack Overflow is a community of 4.7 million programmers, just like you, helping each other. Join them; it only takes a minute: Sign up What does 'stale file handle' in Linux means? [closed] up vote 18 down vote favorite 2 Say I have a terminal open, and fatal error through that terminal I have cd'ed to some directory. Through another terminal, I delete that directory and restore it back from an identical backup. When I try to vim a file from the first terminal, in the same directory, why do I get an error about a stale file handle? What does it mean? (On a side note, I have found that it is possible to bypass this issue through cd $(pwd).) linux unix fatal error chdir share|improve this question asked Nov 20 '13 at 19:34 S.T.A.L.K.E.R. 69221024 closed as off-topic by Vorsprung, pilcrow, Kevin Panko, Salvador Dali, Robin Green Nov 21 '13 at 6:47 This question appears to be off-topic. The users who voted to close gave this specific reason:"Questions about general computing hardware and software are off-topic for Stack Overflow unless they directly involve tools used primarily for programming. You may be able to get help on Super User." – pilcrow, Robin GreenIf this question can be reworded to fit the rules in the help center, please edit the question. add a comment| 1 Answer 1 active oldest votes up vote 23 down vote accepted When the directory is deleted, the inode for that directory (and the inodes for its contents) are recycled. The pointer your shell has to that directory's inode (and its contents's inodes) are now no longer valid. When the directory is restored from backup, the old inodes are not (necessarily) reused; the directory and its contents are stored on random inodes. The only thing that stays the same is that the parent directory reuses the same name for the restored directory (because you told it to). Now if you attempt to access the contents of the directory that your original shell is still pointing to, it communicates that request to the file syste