Open hiro0426 opened 4 years ago
Are you compiling the latest version or the version tagged at v0.4.3? I actually recommend the latter as it is the version directly referenced in the publication and has a better build system suited for just building CANDOCK. Second, the PATH
variable does not help find dynamic libraries, you need to export either LIBRARY_PATH
or LD_LIBRARY_PATH
instead, but I am not sure which one is correct as I do not fully understand the issue given the information provided.
I tried to compile the version tagged at v0.4.3 and was able to compile candock. Thank you for your help. I have another question about using this program. I tried to used find_centroids.sh, but the following error occurred.
GRID> Allocating memory and determining size of grid in /home/apps/candock-941293c3eeafe3184a11e8079ebe8255653074e8/lib/probis/grid.cc:72 minCrd = -28.27 2.43 0.34 in /home/apps/candock-941293c3eeafe3184a11e8079ebe8255653074e8/lib/probis/grid.cc:85 maxCrd = 29.50 58.22 57.13 in /home/apps/candock-941293c3eeafe3184a11e8079ebe8255653074e8/lib/probis/grid.cc:86 cells = 19 18 18 in /home/apps/candock-941293c3eeafe3184a11e8079ebe8255653074e8/lib/probis/grid.cc:87 GRID> Time = 0.00 in /home/apps/candock-941293c3eeafe3184a11e8079ebe8255653074e8/lib/probis/grid.cc:103 Setting descriptors ... Deleting descriptors ... in /home/apps/candock-941293c3eeafe3184a11e8079ebe8255653074e8/lib/probis/desc.cc:258 Deleted 612 descriptors ... in /home/apps/candock-941293c3eeafe3184a11e8079ebe8255653074e8/lib/probis/desc.cc:274 Deleting probe atoms ... in /home/apps/candock-941293c3eeafe3184a11e8079ebe8255653074e8/lib/probis/probe.cc:143 ..deleted 2758 probe atoms. in /home/apps/candock-941293c3eeafe3184a11e8079ebe8255653074e8/lib/probis/probe.cc:152 GRID> Deallocating memory in /home/apps/candock-941293c3eeafe3184a11e8079ebe8255653074e8/lib/probis/grid.cc:111 GRID> Time = 0.00 in /home/apps/candock-941293c3eeafe3184a11e8079ebe8255653074e8/lib/probis/grid.cc:132 Error (STATES) : Cannot open SURF_FILE bslibdb/bslib.txt! Grid destructor in /home/apps/candock-941293c3eeafe3184a11e8079ebe8255653074e8/lib/molib/grid.hpp:161 die : something went wrong in probis ...
I'd appreciate it if you could enlighten me.
First, it appears that you have compiled CANDOCK in DEBUG mode, this will make it very very slow. To build in RELEASE mode, run cmake -DCMAKE_BUILD_TYPE=RELEASE
.
Second, you must obtain a copy of the ProBIS library to use binding site detection (I cannot give you a copy, it is not my data). To proide your own binding site, see the following Perl script:
#!/usr/bin/env perl
use warnings;
use strict;
my $binding_site = 1;
my $one_site = 0;
my $radius = 4.5;
use Getopt::Long;
GetOptions( "r|radius=f" => \$radius,
"o|onesite" => \$one_site );
while ( <> ) {
if (/^(?<atomif> .{6})\s{0,4}
(?<atomid> \d{1,5})\s{1,2}
(?<atomtype> [ A-Z | 0-9 | \d | \s | \' ] {3} )?
(?<alterloc> [ A-Z | \s ])
(?<resn> [ A-Z | \d ] {3} )\s
(?<chain> [ A-Z ] ) \s*
(?<resi> \d{1,4}) \s+
(?<x> -?\d{1,3}\.\d{3} )\s*
(?<y> -?\d{1,3}\.\d{3} )\s*
(?<z> -?\d{1,3}\.\d{3} )\s*
/x) {
next unless $+{atomif} eq "HETATM";
next if $+{resn} eq "HOH";
next if $+{resn} eq " CA";
next if $+{resn} eq " MG";
next if $+{resn} eq " K";
print "$binding_site " unless $one_site;
print "1 " if $one_site;
print "$+{x} $+{y} $+{z} $radius\n";
}
$binding_site++ if eof;
}
The input to the file is a PDB file of a ligand in the binding site of your protein. Save the output of the file as site.cen
and give the location of the file as the parameter to --centroid
.
I have been trying to compile candock in CentOS8 and I keep getting fatal error message saying /usr/bin/ld: warning: libOpenMM.so, needed by /usr/local/lib/libstatchem.so, not found (try using -rpath or -rpath-link). I confirmed that I added the path for libOpenMM.so (PATH="$PATH":/usr/local/openmm/lib in .bashrc). Is there a help topic or something that would help me with the compiling steps ?
Thank you in advance.
Hiroyuki