[gmx-users] Re: Dificulties compiling Gromacs 4.0.2 with MOPAC7 QM/MM, (Laercio Pol Fachin)

Gerrit Groenhof ggroenh at gwdg.de
Thu Dec 11 14:51:34 CET 2008


>
>
> 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  -lxml2  -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 <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Dificulties compiling Gromacs 4.0.2 with
> 	MOPAC7 QM/MM
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <493DC961.4000808 at anu.edu.au>
> 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" <wangjy at ciac.jl.cn>
> Subject: [gmx-users] how to compute the solvent density distribution
> 	around	solute and visulize it
> To: "gmx-users" <gmx-users at gromacs.org>
> Message-ID: <428835785.01298 at eyou.net>
> 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
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡wangjy at ciac.jl.cn
> ¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡¡2008-12-09
>
> ------------------------------
>
> Message: 3
> Date: Tue, 9 Dec 2008 11:18:32 -0500
> From: "Robert Johnson" <bobjohnson1981 at gmail.com>
> Subject: [gmx-users] Relative Binding Free Energy Calculation
> To: "Gromacs Mailing List" <gmx-users at gromacs.org>
> Message-ID:
> 	<b302c1a40812090818x70bd3e00q81aedc0c38eb44f4 at mail.gmail.com>
> 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" <fileti at ufabc.edu.br>
> Subject: [gmx-users] Free energy of transfer with accuracy
> To: gmx-users at gromacs.org
> Message-ID:
> 	<65e289a20812090941p2ada3403l419a5966447ff909 at mail.gmail.com>
> 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 <aroberts99163 at yahoo.com>
> 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 at gromacs.org>
> Message-ID: <5FF3A930-90D5-4DB0-B1D6-AF5643D699F7 at yahoo.com>
> 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" <jalemkul at vt.edu>
> 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 at gromacs.org>
> Message-ID: <493EB5A2.6030206 at vt.edu>
> 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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>>     
>
>   




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