Today's Topics:
Well, I removed that line, and "make" gone further, but I stopped in other
error:
---
make[3]: Entrando no diretório `/usr/local/gromacs-4.0.2/src/kernel'
/bin/sh ../../libtool --tag=CC  --mode=link mpicc -O3 -fomit-frame-pointer
-finline-functions -Wall -Wno-unused -funroll-all-loops  -o grompp grompp.o
libgmxpreprocess_mpi.la ../mdlib/libmd_mpi.la ../gmxlib/libgmx_mpi.la -lxml2Â
-lnsl -lfftw3f -lm  -lSM -lICE -lX11
mpicc -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused
-funroll-all-loops -o grompp grompp.o ./.libs/libgmxpreprocess_mpi.a
../mdlib/.libs/libmd_mpi.a ../gmxlib/.libs/libgmx_mpi.a /usr/lib/libxml2.so -lz
-lnsl -lfftw3f -lm /usr/lib/libSM.so /usr/lib/libICE.so /usr/lib/libX11.so
/usr/lib/libxcb-xlib.so /usr/lib/libxcb.so /usr/lib/libXau.so
/usr/lib/libXdmcp.so -ldl
../mdlib/.libs/libmd_mpi.a(qm_mopac.o): In function `call_mopac_SH':
qm_mopac.c:(.text+0x286): undefined reference to `domop_'
../mdlib/.libs/libmd_mpi.a(qm_mopac.o): In function `call_mopac':
qm_mopac.c:(.text+0x83a): undefined reference to `domop_'
../mdlib/.libs/libmd_mpi.a(qm_mopac.o): In function `init_mopac':
qm_mopac.c:(.text+0xc03): undefined reference to `domldt_'
collect2: ld returned 1 exit status
make[3]: ** [grompp] Erro 1
make[3]: Saindo do diretório `/usr/local/gromacs-4.0.2/src/kernel'
make[2]: ** [all-recursive] Erro 1
make[2]: Saindo do diretório `/usr/local/gromacs-4.0.2/src'
make[1]: ** [all] Erro 2
make[1]: Saindo do diretório `/usr/local/gromacs-4.0.2/src'
make: ** [all-recursive] Erro 1
---
Is there something I should do (better, I forgot to do)?
Did you use the gromacs adapted mopac sources? If not, please retreive
them from the website (below).
Alternatively, you seem to have forgotten to set the LIBS to -lmopac and
LDFLAGS to the location of the mopac library.
Gerrit
Thanks in advance,
Laércio
Message: 2
Date: Tue, 09 Dec 2008 12:26:57 +1100
From: Mark Abraham <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Dificulties compiling Gromacs 4.0.2 with
MOPAC7 QM/MM
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=UTF-8; format=flowed
Laercio Pol Fachin wrote:
Dear GMX users:
I'm facing problems installing Gromacs 4.0.2 with mopac7 QM/MM.
I have downloaded MOPAC7 for SourceForge, as linked in previous mails,
and installed it. After, MPICH and fftw 3.0.1. So: "./configure
--enable-mpi --with-qmmm-mopac" runs O.K., but, during
"make":
(some shell indications in Portuguese):
---
make[3]: Entrando no diretório `/usr/local/gromacs-4.0.2/src/mdlib'
/bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H
-I. -I../../src -I/usr/include/libxml2 -I../../include
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3
-fomit-frame-pointer
-finline-functions -Wall-Wno-unused -funroll-all-loops -MT qm_mopac.lo
-MD -MP -MF .deps/qm_mopac.Tpo -c -o qm_mopac.lo qm_mopac.c
mpicc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2
-I../../include
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3
-fomit-frame-pointer -finline-functions -Wall -Wno-unused
-funroll-all-loops -MT qm_mopac.lo -MD -MP -MF .deps/qm_mopac.Tpo -c
qm_mopac.c -o qm_mopac.o
qm_mopac.c:52:17: error: nsb.h: Arquivo ou diretório não encontrado
My Portuguese is not so hot, but I figure this error translates as
"nsb.h: File or directory not found". That means what it says.
GROMACS
version 3.3.x had this file, version 4.x doesn't. I had a look at
qm_mopac.c and I don't think it was using any of the contents of nsb.h,
so you should be safe to remove this line from qm_mopac.c. Do let us
know how you get on.
Mark
Veja quais são os assuntos do momento no Yahoo! +Buscados
http://br.maisbuscados.yahoo.com
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Message: 2
Date: Tue, 9 Dec 2008 23:21:31 +0800
From: "Jinyao Wang" <[EMAIL PROTECTED]>
Subject: [gmx-users] how to compute the solvent density distribution
around solute and visulize it
To: "gmx-users" <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="gb2312"
gmx-usershello,gmx-users
I would like to compute the solvent density distribution around solute and visualize the solvent density maps around solute. I have read the manual and known the g_densmap could do it. I have carried out the g_densmap as follow,
g_densmap -f traj.xtc -s topol.tpr -n index.ndx -bin 0.1 -n1 6 -n2 6 -amax 3 -rmax 6 -mirror -unit count -o densmap.xpm
xpm2gs -f densmap.xpm -nice 10 -size 400 -rainbow -o plot.eps
But the plot.eps is not the figure in the link http://p13.freep.cn/p.aspx?u=v20_p13_p_0812092310359766_0.jpg
I want to know more details about how to get the figure in the link. it is appreciated if you could give me some suggestion
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡Jinyao Wang
[EMAIL PROTECTED]
¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2008-12-09
------------------------------
Message: 3
Date: Tue, 9 Dec 2008 11:18:32 -0500
From: "Robert Johnson" <[EMAIL PROTECTED]>
Subject: [gmx-users] Relative Binding Free Energy Calculation
To: "Gromacs Mailing List" <gmx-users@gromacs.org>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1
Hello everyone,
When performing a relative binding free energy calculation, I
understand that it is a good practice to separate the transformation
of charges of the ligand and the transformation of vdW parameters into
two calculations. However, is it advisable to completely discharge the
ligand before transforming vdW parameters? For example, should the
calculation proceed as:
1. Reduce all ligand charges to zero
2. Transform vdW parameters for relevant atoms
3. Recharge ligand atoms with the new, appropriate values
It seems to me that steps 1 and 3 would yield large free energy
changes, thus making the calculation of free energy differences
between the bound and unbound states more difficult due to convergence
issues. Is it more advisable to proceed as:
1. Reduce charges to zero on ONLY those ligand atoms that will have
their vdW parameters transformed
2. Transform vdW parameters for relevant atoms
3. Transform charges on ligand to their new, appropriate values
Proceeding in this way seems like you would obtain smaller free energy
changes for steps 1 and 3 and could result in better convergence for
free energy differences. Any suggestions?
Thanks,
Bob
------------------------------
Message: 4
Date: Tue, 9 Dec 2008 15:41:25 -0200
From: "Eudes Fileti" <[EMAIL PROTECTED]>
Subject: [gmx-users] Free energy of transfer with accuracy
To: gmx-users@gromacs.org
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
Hi gmx-users,
I have tried to calculate the free energy of transfer of
a solute between two solvents by thermodynamic integration.
However, the dgdl plot I have obtained is not smooth enough to ensure
accuracy.
I have used a non homogeneous spacing for lambda. The first is from 0.0 to
0.4 (dl=0.04),
the second is from 0.405 to 0.48 (dl=0.005) and the third is from 0.48 to 1
(dl=0.04).
Overall, I was performed 40 simulations.
As can be seen in the figure (
http://cromo.ufabc.edu.br/~fileti/web/dgdl-transfer.jpg ),
there is a large fluctuation in the region that goes from 0.40 to 0.48.
Each simulation was carried out by 0.5ns preceded by 0.15ns of
equilibration.
I am using soft-core whose parameters are:
; Free energy control stuff
free_energy = yes
init_lambda = 0.00
delta_lambda = 0
sc_alpha = 1.3
sc-power = 1.0 (for this I also used 2).
sc-sigma = 0.47
In the example of the link sc-power=1, but I re-did the calculations with
sc-power=1
and I found the same behavior (although the format of the plot was a little
different).
Can you suggest me a way to calculate this free energy difference with
accuracy?
The perturbation free energy method could give better results?
Thank you
EEF
_______________________________________
Eudes Eterno Fileti
Centro de Ciências Naturais e Humanas
Universidade Federal do ABC
Rua Santa Adélia, 166 - Bloco B, Sala 1048
09210-170 Santo André - SP Brasil
+55.11.4437-8408
skype: eefileti
http://cromo.ufabc.edu.br/~fileti/
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Message: 5
Date: Tue, 9 Dec 2008 10:05:12 -0800
From: Arthur Roberts <[EMAIL PROTECTED]>
Subject: [gmx-users] Is there a way to add protons to all the residues
in a pdb file that was run with the protons missing?
To: gmx users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
Hi, all,
This is probably an obvious question. I did a simulation with an
ff53a6 force field, which lacks protons on aliphatic side chains. I
have pdb coordinates for each time. Is there a way to add protons to
the aliphatic side chains. Your input is appreciated.
Sincerely,
Art Roberts
------------------------------
Message: 6
Date: Tue, 09 Dec 2008 13:14:58 -0500
From: "Justin A. Lemkul" <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] Is there a way to add protons to all the
residues in a pdb file that was run with the protons missing?
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Arthur Roberts wrote:
Hi, all,
This is probably an obvious question. I did a simulation with an ff53a6
force field, which lacks protons on aliphatic side chains. I have pdb
coordinates for each time. Is there a way to add protons to the
aliphatic side chains. Your input is appreciated.
Did you not receive my last message?
http://www.gromacs.org/pipermail/gmx-users/2008-December/038513.html
-Justin
Sincerely,
Art Roberts
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