|
|
Bioinformatics.org
|
![[?]](https://www.bioinformatics.org/images/icons/info.png)
|
|
Research
|
Online databases
Online analysis tools
Online education tools
|
|
Development
|
|
|
Forums
|
News & Commentary
Jobs Forum
(Career Center)
|
|
|
Ghemical: Molecular modelling - Message forums
|
         
|
 |
|
Expanded view | Monitor forum | Save place
|
|
|
|
I import an mm 1 gp file into the qm 1 gp project, I try to compute the molecules energy, but as soon as I select "energy" the entire program shuts down.
I noticed the /home/xxx/mpqc-target/lib during the first make of installation, and I realized that I had to copy all the files of /home/xxx/mpqc-1.2.5 and paste them into /home/xxx/mpqc-target.
Do other mpqc files need to copied and pasted in other folders as well?
Please, if you have any suggestions let me know...
I love the program so far...
|
|
|
|
|
|
Hi, and sorry for the late answer. Haven't checked this for a while, so if you don't get response here please use email instead.
Did you compile your MPQC as explained in the INSTALL file? You see, no parallelization can be used in MPQC, and those features must be disabled when configuring/compiling it.
At aug/sep we will roll out a new version 0.80 with much improved QM features, including a built-in MOPAC7 for semiempirical methods. :-)
TH
|
|
|
|
|
|
Hi,
I downloaded ghemical-0.80.tgz to my RH 7.1 box together with
the packages listed in INSTALL instructions. The compilation
ran nicely up to linker
g++ -o /home/nick/tars/ghemical-0.80/bin/ghemical ...
where I got a long list of undefined reference from
miniMOPAC/ package. These are
/* Builtin functions */
integer i_indx(), s_wsfe(), do_fio(), e_wsfe();
I wonder what are these builtin functions and which
library I am missing now.
If you have any suggestion, please let me know.
Thanks in advance, Nikolai
(e-mail: nikolai.tkachenko@tut.fi)
|
|
|
|
|
|
Hi,
are you sure that you have the f2c (fortran to c translating utility) installed; that's an rpm package at powertools CD of RedHat 7.1.
In linking you need a libg2c library that is included to the f2c package; you can check it's presence also this way:
$ locate libg2c
/usr/lib/gcc-lib/i386-redhat-linux/2.96/libg2c.a
Tommi
|
|
|
|
|
|
Hi,
are you sure that you have the f2c (fortran to c translating utility) installed; that's an rpm package at powertools CD of RedHat 7.1.
In linking you need a libg2c library that is included to the f2c package; you can check it's presence also this way:
$ locate libg2c
/usr/lib/gcc-lib/i386-redhat-linux/2.96/libg2c.a
Tommi
|
|
|
|
|
|
Thanks for help Tommi!
The libg2c.a library was missing Makefile
(actually in Makefile.in). Now it is compiled.
Ghemical works fine and looks great!
So far I have one another question:
is there any docs about using the program
for molecular mechanisc and quantum mechanics
computations?
Thank you once again, Nikolai
|
|
|
|
|
|
Hi,
there are some documentation in the User's Manual, and you can find it from the Help/Help of main menu, or from directory bin/user-docs at the source tree.
|
|
|
|
|
|
Hi!
I've downloaded ghemical 0.80 and i've compiled it on my Intel Celeron Mendoccino(@450Mhz) machine running Mandrake Linux 8.0.The program looks and works quite fine execpt for one problem::after i play a little with the molecule and do some rendering and ESP-surface I get A LOT of hard drive activity.It consumes all the system's resourses (I can't do nothing even open another aplication or sometimes move the mouse).This take place for about 20 mins, and then it stops.During this 20 min period.I can't do nothing except restarting the computer manually...
Please help me!Thanks!
P.Splease answer me if you can by sending a mail to this adress:_mad_@metacrawler.com
|
|
|
|
|
|
I'd certainly check the most recent (0.81) release, which fixes a variety of memory leaks. If the memory consumption causes VM to kick in, this would certainly explain your problems.
-Geoff
|
|
|
|
|
|
dear all
i've been trying to compile ghemical 0.90 but I get error messages in the graphics/ dir. i've got GLUT 3.7 on my system and have experienced no problems until now. there are comments in views.cpp mentioning some versions of GLUT have no support for bitmap fonts. is this the problem? how do I fix it? the cvs version doesn't seem to behave any different.
please help
thanks
this is what I get from make:
/home/nacos/ghemical-0.90/src/graphics/./views.cpp:102: undefined reference to `glutBitmapWidth'
/home/nacos/ghemical-0.90/src/graphics/./views.cpp:103: undefined reference to `glutStrokeRoman'
/home/nacos/ghemical-0.90/src/graphics/./views.cpp:103: undefined reference to `glutStrokeWidth'
../..//src/graphics/libgraphics.a(views.o): In function `ogl_view::WriteGlutString3D(char const *, float, float, float, obj_loc_data const *, void *)':
/home/nacos/ghemical-0.90/src/graphics/./views.cpp:145: undefined reference to `glutBitmapCharacter'
/home/nacos/ghemical-0.90/src/graphics/./views.cpp:167: undefined reference to `glutStrokeRoman'
/home/nacos/ghemical-0.90/src/graphics/./views.cpp:167: undefined reference to `glutStrokeCharacter'
../..//src/graphics/libgraphics.a(views.o): In function `enlevdiag_view::Render(void)':
/home/nacos/ghemical-0.90/src/graphics/./views.cpp:630: undefined reference to `glutBitmapTimesRoman24'
/home/nacos/ghemical-0.90/src/graphics/./views.cpp:766: undefined reference to `glutBitmapTimesRoman10'
../..//src/graphics/libgraphics.a(qm1docv.o): In function `qm1_docv::Render(graphics_view *, docview::rmode)':
/home/nacos/ghemical-0.90/src/graphics/./qm1docv.cpp:287: undefined reference to `glutBitmap9By15'
../..//src/graphics/libgraphics.a(mm1docv.o): In function `mm1_docv::Render(graphics_view *, docview::rmode)':
/home/nacos/ghemical-0.90/src/graphics/./mm1docv.cpp:244: undefined reference to `glutBitmap9By15'
/home/nacos/ghemical-0.90/src/graphics/./mm1docv.cpp:261: undefined reference to `glutBitmap9By15'
/home/nacos/ghemical-0.90/src/graphics/./mm1docv.cpp:278: undefined reference to `glutBitmap9By15'
/home/nacos/ghemical-0.90/src/graphics/./mm1docv.cpp:295: undefined reference to `glutBitmap9By15'
../..//src/graphics/libgraphics.a(mm1docv.o):/home/nacos/ghemical-0.90/src/graphics/./mm1docv.cpp:312: more undefined references to `glutBitmap9By15' follow
|
|
|
|
|
|
I have compiled ghemical 0.90 using
Mesa-3.4.2-7
Mesa-devel-3.4.2-7
on an i386 Red Hat 7.2 system.
I had no problems with the compilation.
|
|
|
|
|
|
Is there an easy way to map the core levels to the atoms? I am trying to extract the C1s core level shifts for different C atoms in a molecule.In the energy level view I can read off the energy levels, but I do not know which level belongs to which atom.
|
|
|
|
|
|
Hi,
and sorry for the late answer; it's easier to reach me using email since I only seldom look at these forums.
So, I understood that you need to relate the inner shell electrons (ab initio/MPQC) to the atoms. Perhaps drawing a plot for these MO's can be used for this; the plots should be local and you can then see in which atoms does it relate.
I don't know any easier way, neither in the GUI nor in the MPQC code.
Regards,
Tommi
|
|
|
|
|
|
Hi,
I am trying to compile ghemical 1.5 on my notebook with g++ 3.2-7 and seem to get stuck at target3.
BTW configure ran fine and did not indicate any problem.
The compilation stops however at t3main.cpp
with In file included from /usr/include/c++/3.2/i386-redhat-linux/bits/c++locale.h:39,
from /usr/include/c++/3.2/bits/localefwd.h:46,
from /usr/include/c++/3.2/ios:48,
from /usr/include/c++/3.2/ostream:45,
from /usr/include/c++/3.2/iostream:45,
from ../../src/common/typedef.h:22,
from ../../src/common/v3d.h:17,
from ../../src/graphics/objects.h:32,
from ../../src/graphics/camera.h:34,
from ../../src/graphics/mtools.h:42,
from ../../src/graphics/views.h:39,
from t3views.h:28,
from t3main.h:19,
from t3main.cpp:10:
/usr/include/libintl.h:40: parse error before `__const'
/usr/include/libintl.h:44: parse error before `__const'
/usr/include/libintl.h:52: parse error before `__const'
/usr/include/libintl.h:81: parse error before `__const'
/usr/include/libintl.h:86: parse error before `__const'
In file included from /usr/include/c++/3.2/backward/strstream:51,
from t3main.cpp:24:
/usr/include/c++/3.2/backward/backward_warning.h:32:2: warning: #warning This file includes at least one deprecated or antiquated header. Please consider using one of the 32 headers found in section 17.4.1.2 of the C++ standard. Examples include substituting the <X> header for the <X.h> header for C++ includes, or <sstream> instead of the deprecated header <strstream.h>. To disable this warning use -Wno-deprecated.
make[1]: *** [t3main.o] Error 1
Does anyone have a clue as to what is going wrong ?
Thanks. Lothar
|
|
|
|
|
|
Hi! I also encountered this problem with gcc-3 and it's solvable (or at least it was in my system :)
Please note that the error occurs in /usr/include/libintl.h which does not belong to ghemical sources but system libraries. The libintl just seems not be gcc-3 compatible yet and it will be fixed, sooner or later.
How I fixed this problem in my system, was that I simply truncated the libintl.h file into a zero length file (since the compilation succeeded even without it). To try the same thing, please first make a backup of libint.h:
cp /usr/include/libintl.h /usr/include/libintl.h_
and then truncate it:
rm /usr/include/libintl.h
touch /usr/include/libintl.h
Ok, that's how I fixed it; but do this at your own risk! ;)
|
|
|
|
|
|
Hello,
I've just compiled MPQC 2.1.5.on Red Hat 9.0. I met the same error, but I fixed it in another way:
-At the mentioned lines I made the following changes:
old: extern char *gettext (__const *...etc)
new: extern char *__gettext (__const * ...etc)
mihai
|
|
|
|
|
|
This is caused by a conflict between the system libintl.h file and the gnulibintl.h file used by gnome. You just need to reorder some of the includes in the file t3views.h. To fix this problem, use the following patch.
diff -urw ghemical-1.50alpha.orig/src/target3/t3views.h ghemical-1.50alpha/src/target3/t3views.h
--- ghemical-1.50alpha.orig/src/target3/t3views.h 2002-05-30 05:29:13.000000000 -0400
+++ ghemical-1.50alpha/src/target3/t3views.h 2004-01-12 17:41:01.000000000 -0500
@@ -21,11 +21,11 @@
/*################################################################################################*/
+#include "views.h"
#include <gtk/gtk.h>
#include <gtkgl/gtkglarea.h>
#include <gnome.h>
-#include "views.h"
#include "t3project.h"
#include <vector>
|
|
|
|
|
|
Hello,
I'm trying to compile on SuSE 8.1 but make always fails:
---snip-----
geomopt_dialog.h:34: candidate is: static void
geomopt_dialog::handler_ButtonOK(...)
geomopt_dialog.cpp: In member function `void
geomopt_dialog::handler_ButtonOK(GtkWidget*, void*)':
geomopt_dialog.cpp:106: `class geomopt_dialog' has no member named `xml'
geomopt_dialog.cpp:107: `class geomopt_dialog' has no member named `xml'
geomopt_dialog.cpp:108: `class geomopt_dialog' has no member named `xml'
geomopt_dialog.cpp:122: `class geomopt_dialog' has no member named `
entry_nsteps'
geomopt_dialog.cpp:127: `class geomopt_dialog' has no member named `entry_grad'
geomopt_dialog.cpp:132: `class geomopt_dialog' has no member named `
entry_delta_e'
geomopt_dialog.cpp:185: `class geomopt_dialog' has no member named `dialog'
geomopt_dialog.cpp: At global scope:
geomopt_dialog.cpp:189: prototype for `void
geomopt_dialog::handler_ButtonCancel(GtkWidget*, void*)' does not match any
in class `geomopt_dialog'
geomopt_dialog.h:35: candidate is: static void
geomopt_dialog::handler_ButtonCancel(...)
geomopt_dialog.cpp: In member function `void
geomopt_dialog::handler_ButtonCancel(GtkWidget*, void*)':
geomopt_dialog.cpp:195: `class geomopt_dialog' has no member named `dialog'
make[1]: *** [geomopt_dialog.o] Fehler 1
make[1]: Verlassen des Verzeichnisses »/usr/src/packages/SOURCES/ghemical-1.00/src/target3/glade«
make: *** [all] Fehler 1
I'm using the standard packages incl. devel-packages provided by SuSE:
gcc-3.2
f2c-0.11
make-3.79.1
mesaglut-4.0.3
gnome-libs-1.4.1.7
gtkglarea-1.2.2
mpqc-1.2.5
Anyone any idea how to fix? Downgrading gnome?
Thanks, Tim
|
|
|
|
|
|
Hi.
Looks like a simple error, but is not. It says
`class geomopt_dialog' has no member named `xml'
but sure there should be such a member.
Sorry, but I have never seen such an error and I can't tell where it comes.
Regards,
Tommi
|
|
|
|
|
|
Im trying to compile 1.50 in 64 Bit Suse 9.0.
"configure" stops with statement, f2c is not in system, but all f2c libraries ARE installed and in path. How could i change "configure" files to recognize the libraries ?
|
|
|
|
|
|
Hello forum,
compiling under Suse 9.3 with gtk-1.2.10, pkgconfig-0.15.0 and gtkglarea-1.2.2 fails:
here's the error:
checking for GTK... configure: error: The pkg-config script could not be found or is too old. Make sure it
is in your PATH or set the PKG_CONFIG environment variable to the full
path to pkg-config.
Alternatively, you may set the environment variables GTK_CFLAGS
and GTK_LIBS to avoid the need to call pkg-config.
See the pkg-config man page for more details.
although I have got pkgconfig as you see.
I also tried setting GTK_CFLAGS and GTK_LIBS environment variables but of no effect.
Could anyone help me with this?
|
|
|
|
|
|
hi here, i want to know where i can get the vibrational frequency in ghemical
thanx and nice day
|
|
|
|
|
|
I can't compile ghemical 2.01. After doing ./configure, I try ./make, and end up with these error-messages:
http://www.physik.fu-berlin.de/~goerz/download/errors.txt
How can I compile it? Alternatively, does anyone have a rpm for a Suse 10.x System?
|
|
|
|
|
|
Hi all,
I was wondering if anyone tried to use PC-Gamess
with ghemical-gms? I modifie the rungms script by replacing all instances of wingamess by PCGAMESS, but still no luck.
This is the output I get from running gtk-gamess:
rm: cannot remove `temp/gamess-input-anchor-thiol.*': No such file or directory
Any comments or help will be useful.
Thanks.
|
|
|
|
|
|
I have a Windows 10 box running Cygwin64. I am trying to run the configure script. The configure script stops with the following problems:
No package 'gtk+-2.0' found
No package 'gtkglext-1.0' found
No package 'libglade-2.0' found
I went to install gtk+ and could not find it in the Cygwin list of packages, but I could find gtk. Installing those packages did not change the termination messages.
Is there someone with experience in using Cygwin and ghemical to point me in the right direction?
Thanks...
|
|
|
Start a new thread:
You have to be to post a reply.
|
|
![[University of Birmingham]](https://www.bioinformatics.org/images/ack_banners/Birmingham-728x90.gif)
![[Patsnap]](https://www.bioinformatics.org/images/ack_banners/Patsnap-728x90.png)