|
|
Flexweb Forum
|
4
|
FIRST - Command-line Version / General Support / Running FIRST with a vdb File Converted to pdb with over 99,999 Atoms
|
on: August 22, 2008, 05:26:16 PM
|
|
Started by gyee1130 | Last post by gyee1130
|
Hi,
We are running a CCMV full capsid pdb file on FIRST. The file was originally a vdb file downloaded from http://viperdb.scripps.edu/ and converted it to pdb file using the hybrid-36 numbering system. The problem we are running into is the following error
*** glibc detected *** ./FIRST: free(): invalid pointer: 0xbff252f4 ***
======= Backtrace: =========
/lib/libc.so.6[0x8f5df1]
/lib/libc.so.6(cfree+0x90)[0x8f9430]
/usr/lib/libstdc++.so.6(_ZdlPv+0x21)[0x35e5091]
/usr/lib/libstdc++.so.6(_ZNSs4_Rep10_M_destroyERKSaIcE+0x1d)[0x35c1c5d]
/usr/lib/libstdc++.so.6(_ZNSs6assignERKSs+0xa6)[0x35c32a6]
./FIRST[0x80be147]
./FIRST[0x80adb03]
./FIRST[0x80b34af]
/lib/libc.so.6(__libc_start_main+0xe0)[0x8a3f70]
./FIRST(__gxx_personality_v0+0xa5)[0x804b281]
======= Memory map: ========
00110000-00111000 r-xp 00110000 00:00 0 [vdso]
0086f000-0088a000 r-xp 00000000 fd:00 131368 /lib/ld-2.6.so
0088a000-0088b000 r-xp 0001a000 fd:00 131368 /lib/ld-2.6.so
0088b000-0088c000 rwxp 0001b000 fd:00 131368 /lib/ld-2.6.so
0088e000-009dc000 r-xp 00000000 fd:00 131375 /lib/libc-2.6.so
009dc000-009de000 r-xp 0014e000 fd:00 131375 /lib/libc-2.6.so
009de000-009df000 rwxp 00150000 fd:00 131375 /lib/libc-2.6.so
009df000-009e2000 rwxp 009df000 00:00 0
009e4000-00a0b000 r-xp 00000000 fd:00 135545 /lib/libm-2.6.so
00a0b000-00a0c000 r-xp 00026000 fd:00 135545 /lib/libm-2.6.so
00a0c000-00a0d000 rwxp 00027000 fd:00 135545 /lib/libm-2.6.so
03531000-03611000 r-xp 00000000 fd:00 1339299 /usr/lib/libstdc++.so.6.0.8
03611000-03614000 r-xp 000e0000 fd:00 1339299 /usr/lib/libstdc++.so.6.0.8
03614000-03616000 rwxp 000e3000 fd:00 1339299 /usr/lib/libstdc++.so.6.0.8
03616000-0361c000 rwxp 03616000 00:00 0
0361e000-03629000 r-xp 00000000 fd:00 131074 /lib/libgcc_s-4.1.2-20070925.so.1
03629000-0362a000 rwxp 0000a000 fd:00 131074 /lib/libgcc_s-4.1.2-20070925.so.1
08048000-081bd000 r-xp 00000000 00:16 19563130 /home/gyee/FIRST6.2/FIRST
081bd000-081be000 rw-p 00175000 00:16 19563130 /home/gyee/FIRST6.2/FIRST
081be000-081bf000 rw-p 081be000 00:00 0
08f71000-0d618000 rw-p 08f71000 00:00 0
b4a00000-b4a21000 rw-p b4a00000 00:00 0
b4a21000-b4b00000 ---p b4a21000 00:00 0
b4bc6000-b7f3d000 rw-p b4bc6000 00:00 0
b7f4e000-b7f4f000 rw-p b7f4e000 00:00 0
bff13000-bff28000 rw-p bffea000 00:00 0 [stack]
Aborted
this is from entering ./FIRST ccmvfull_vdb_master.pdb -non -L /home/gyee/FIRST6.2/
at the command line. I ran it without adding the hydrogen bonds, but I do not think it should not have caused this error. The pdb file was too large to post here, so you'll have to download it from here http://www.wikiupload.com/download_page.php?id=54452
|
|
|
6
|
FIRST - Command-line Version / Developer's Corner / ERROR: memory leak in PebbleGame found
|
on: June 10, 2008, 12:37:20 PM
|
|
Started by rader | Last post by rader
|
I found a memory leak in the PebbleGame program. This was found because of a segmentation fault of certain Ecut values for certain pdb files. I'll attach one.
If you run it using the following options:
FIRST -non -E -2.0 1y8nI.pdb -v 3
everything is fine, but if you use the following option:
FIRST -non -E -2.1 1y8nI.pdb -v 3
then a segfault involving the following invalid pointer call occurs and the screen output is as follows.
[font=Verdana][color=Blue]
|
|
|
8
|
FIRST - Command-line Version / Developer's Corner / nosterics flag not working?
|
on: May 19, 2008, 05:33:09 PM
|
|
Started by craig | Last post by craig
|
Hey...
Nothing seems to run correctly with the -nosterics flag. Regardless of what file I run (I've tried a few) the last lines of my output are:
Initializing FRODA...
Defining side and main clusters.
Simulating 1000 configurations.
Outputing every 100th conformation.
Segmentation fault
when I use the command line
~/FIRST/src/FIRST -FRODA -nosterics 1000.pdb
I'll try and get this fixed, but if anyone else has seen this I'd appreciate knowing.
|
|
|
9
|
Flexweb / News and Updates / Structures with more than 99,999 atoms
|
on: April 11, 2008, 02:53:14 PM
|
|
Started by kirill | Last post by kirill
|
FIRST/FRODA code was modified to implement Hybrid-36 (http://cci.lbl.gov/hybrid_36/) PDB format. Now PDB files can handle up to 87,440,031 ATOM with unique serial numbers and up to 24,36,111 residue sequence numbers per chain. The difference between "traditional" and hybrid-36 PDB files becomes evident only if there are more than 99,999 atoms in the file.
The processing of a structure with more than 99,999 atoms with FRODA will be available only on stand alone FIRST/FRODA, the on-line version of FRODA will stay with processing of structures with less than 99,999 atoms. On-line FIRST will be able to analyze structures with more than 99,999 atoms.
It is possible to upload zipped PDB stucture to web FIRST/FRODA.
I added encode_hybrid_36.py Python script to util directory and attached it to this post. This script converts PDB files to hybrid-36 format.
Please test out large PDB structures and let me know if you notice any problems with it.
|
|
|
10
|
FIRST - Command-line Version / General Support / Re: RNA conformational space
|
on: March 25, 2008, 11:44:34 AM
|
|
Started by rambor | Last post by rambor
|
Just to be in the spirit of answering myself. I found an interesting paper from Fulle, S. and Gohlke H. titled "Analyzing the flexibility of RNA structures by constraint counting".
The authors argue "... that because FRODA generates new conforms by satisfying existing constraints, only local motions consistent with the analyzed constraint network can be observed. Large conformational movements frequently observed in RNA that require changes in the constraint network cannot be detect this way."
Is this true? I am a newbie to FIRST/FRODA and my family of structures do not show significant changes in the RNA structure. However, it may be due to parameters I am using but it seems to show that my RNA is trapped in an energy well... I don't know. I just want to generate a large family of structures based on a crystal structure.... my journey continues.
|
|
Return to the board index.
|
|
