[gmx-users] Can not open file: topol.tpr

J. Rui Rodrigues joaquim.rodrigues at estg.ipleiria.pt
Tue Mar 3 13:59:39 CET 2009 

It's not mdrun -v deffnm em, but:
mdrun -v -deffnm em

Rui




On Tue, 03 Mar 2009 15:52:36 +0300, drugdesign wrote
> Oh, I am very sorry, I've copied the wrong error. Actually error was with the 
> same tutorial at the next step with mdrun -v deffnm em. I can't figure  out 
> why I need topol.tpr for energy minimization? It must be only em.tpr, right? 
> by -v deffnm command?
> 
> -------------------------------------------------------
> Program mdrun, VERSION 4.0.2
> Source code file: gmxfio.c, line: 736
> 
> Can not open file:
> topol.tpr
> -------------------------------------------------------
> 
> "I Smell Smoke From a Gun Named Extinction" (Pixies)
> 
> andrew at linux-f29d:~/GROMACS_MD/1LYD> mdrun -v deffnm em
> 
> -------- [UTF-8?]Пересылаемое [UTF-8?]сообщение --------
> 02.03.09, 00:19, gmx-users-request at gromacs.org:
> 
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> Today's Topics:
> 
>    1. Question (Elias santos)
>    2. tool.top does not found (drugdesign)
>    3. Re: tool.top does not found (Justin A. Lemkul)
>    4. help with FAD topology, please (Miguel Quiliano Meza)
>    5. Re: help with FAD topology, please (Justin A. Lemkul)
>    6. Re: Question (Mark Abraham)
>    7. RE: Cannot obtain the expected pressure using the
>       Parrinello-Rahman coupling in a gas-liquid system (Berk Hess)
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Sun, 1 Mar 2009 09:14:36 -0300
> From: Elias santos <silvasantosster at gmail.com>
> Subject: [gmx-users] Question
> To: gmx-users-request <gmx-users-request at gromacs.org>,	gmx-users
> 	<gmx-users at gromacs.org>
> Message-ID:
> 	<97baf6380903010414v50f35a14l47d66fbf020a2fdb at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi!!
> 
> I am changing my equipment for a AMD quad Core with two physical
> processors and would like to know if in this configuration I will have
> problems of compatibility with gromacs 4.0.
> 
> Elias Silva
> 
> ------------------------------
> 
> Message: 2
> Date: Sun, 01 Mar 2009 17:07:25 +0300
> From: drugdesign <drugdesign at yandex.ru>
> Subject: [gmx-users] tool.top does not found
> To: gmx-users at gromacs.org
> Message-ID: <29071235916445 at webmail45.yandex.ru>
> Content-Type: text/plain; charset=KOI8-R
> 
> Dear GROMACS users,
> I am trying to perform [UTF-8?]thе tutorial listed below with amber03 force field,
>  but I get an error about tool.top while running grompp with em.mdp What can 
> cause such a problem? Best regards, Andrew
> 
> https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf
> 
> This is a command line:
> 
> andrew at linux-f29d:~/GROMACS_MD/1LYD> grompp -f em.mdp -p tool.top -c 
> solvated.gro -o em.tpr
> 
> checking input for internal consistency...
> 
> -------------------------------------------------------
> Program grompp, VERSION 4.0.2
> Source code file: grompp.c, line: 810
> 
> Fatal error:
> tool.top does not exist
> -------------------------------------------------------
> 
> "Baseball Heroes Only" (P.J. Harvey)
> 
> ------------------------------
> 
> Message: 3
> Date: Sun, 01 Mar 2009 09:54:11 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] tool.top does not found
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <49AAA193.4050303 at vt.edu>
> Content-Type: text/plain; charset=KOI8-R; format=flowed
> 
> drugdesign wrote:
> > Dear GROMACS users,
> > I am trying to perform [UTF-8?]thе tutorial listed below with amber03 force field, but I get an error
> > about tool.top while running grompp with em.mdp
> > What can cause such a problem?
> > Best regards,
> > Andrew
> > 
> > https://extras.csc.fi/chem/courses/gmx2007/tutorial1/tutorial1.pdf 
> > 
> > This is a command line:
> > 
> > andrew at linux-f29d:~/GROMACS_MD/1LYD> grompp -f em.mdp -p tool.top -c solvated.gro -o em.tpr
> > 
> > checking input for internal consistency...
> > 
> > -------------------------------------------------------
> > Program grompp, VERSION 4.0.2
> > Source code file: grompp.c, line: 810
> > 
> > Fatal error:
> > tool.top does not exist
> > -------------------------------------------------------
> >
> 
> tool.top != topol.top; watch for typos!
> 
> -Justin
> 
> > "Baseball Heroes Only" (P.J. Harvey)
> > 
> > 
> > 
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 
> ------------------------------
> 
> Message: 4
> Date: Sun, 1 Mar 2009 11:42:04 -0500
> From: Miguel Quiliano Meza <rifaximina at gmail.com>
> Subject: [gmx-users] help with FAD topology, please
> To: gmx-users at gromacs.org
> Message-ID:
> 	<6c2f55e30903010842g462991c8nf4fe6189dfb34e1c at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Dear all.
> 
> I am a new user of GROMACS, I have read the user book and free tutorials in
> the WEB, but now when I try to do a simulation, appears FAD no topology, I
> have been reading that PRODRG server is a way to achieve that goal, I tried
> but the output format is different, it means old version (for gromos 96
> forcefield).
> 
> I do not mind edit by hand (I want to learn), I searched in the gmx-users
> but no one shares the  FAD topology. Until now, I can't run my simulation.
> 
> So, I would be very grateful if someone could give me "tips", advices or the
> FAD topology (in this way I could see my errors).
> 
> Thanks in advance.
> 
> Miguel.
> -------------- next part --------------
> An HTML attachment was scrubbed...
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> 
> ------------------------------
> 
> Message: 5
> Date: Sun, 01 Mar 2009 11:53:14 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] help with FAD topology, please
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <49AABD7A.2030300 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Miguel Quiliano Meza wrote:
> > Dear all.
> >  
> > I am a new user of GROMACS, I have read the user book and free tutorials 
> > in the WEB, but now when I try to do a simulation, appears FAD no 
> > topology, I have been reading that PRODRG server is a way to achieve 
> > that goal, I tried but the output format is different, it means old 
> > version (for gromos 96 forcefield).
> >
> 
> PRODRG will give ffgmx-compatible output, but PRODRG beta will give 
> Gromos96-compatible output.  The latter is preferred, but in either case you 
> will have to manually alter the topology.
> 
> > I do not mind edit by hand (I want to learn), I searched in the 
> > gmx-users but no one shares the  FAD topology. Until now, I can't run my 
> > simulation.
> >
> 
> In the .rtp file of several Gromos96 force fields you will find a few 
> different FMN variants.  This should provide you with a reasonable starting 
> point for creating your FAD topology (when you consider that ATP is also part 
> of the force field as well).
> 
> -Justin
> 
> > So, I would be very grateful if someone could give me "tips", advices or 
> > the FAD topology (in this way I could see my errors).
> >  
> > Thanks in advance.
> >  
> > Miguel.
> > 
> > 
> > ------------------------------------------------------------------------
> > 
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before posting!
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> -- 
> ========================================
> 
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
> ========================================
> 
> ------------------------------
> 
> Message: 6
> Date: Mon, 02 Mar 2009 04:59:51 +1100
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Question
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <49AACD17.20503 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Elias santos wrote:
> > Hi!!
> > 
> > I am changing my equipment for a AMD quad Core with two physical
> > processors and would like to know if in this configuration I will have
> > problems of compatibility with gromacs 4.0.
> 
> No - MPI will be needed, but that is a non-issue.
> 
> Mark
> 
> ------------------------------
> 
> Message: 7
> Date: Sun, 1 Mar 2009 22:18:51 +0100
> From: Berk Hess <gmx3 at hotmail.com>
> Subject: RE: [gmx-users] Cannot obtain the expected pressure using the
> 	Parrinello-Rahman coupling in a gas-liquid system
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <BLU134-W328EB76CCB30D2D512D8F08EA80 at phx.gbl>
> Content-Type: text/plain; charset="gb2312"
> 
> Hi,
> 
> But this has nothing to do with bug 165, does it?
> 
> If you have a surface, you have surface tension which tries to minimize the 
> surface area. That is what you should get and what you indeed do get; x/y get 
> smaller, z gets larger, decreasing the surface area.
> 
> If you have a x/y surface, you should keep the x/y sizes constant and only 
> couple z.
> 
> Berk
> 
> From: guogj at hotmail.com
> To: gmx-users at gromacs.org
> Subject: RE: [gmx-users] Cannot obtain the expected pressure using the	
> Parrinello-Rahman coupling in a gas-liquid system
> Date: Sun, 1 Mar 2009 05:09:39 +0000
> 
> Hi,
> 
> After I recheck the box, it is indeed the case described in bugzilla 165. The 
> length of box increases in the Z-direction and decreases in the X/Y-direction 
> with time. When I prolong the run, it exits abnormally at the time when the 
> Box-X/Y reduces to a value less than 2*rvdw. When I fix the Box-Z by setting 
> the compressibility as zero, the semiisotropic with P-R barostat produces the 
> inaccurate pressure again. Now, I have to use the Berendsen barostat for my 
> methane-water interface system.
> 
> Guang-Jun
> 
> > Date: Sat, 28 Feb 2009 19:53:10 +0100
> > From: spoel at xray.bmc.uu.se
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] Cannot obtain the expected pressure using the Parrinello-Rahman coupling in a 
gas-liquid system
> > 
> > GuoGuangjun wrote:
> > > Hi,
> > > 
> > > 
> > > The question is resolved by changing the pcoupltype from isotropic to 
> > > semiisotropic. Correspondingly, the compressibility and ref_p are given 
> > > for the x/y and z directions with the same original values, 
> > > respectively. The test system includes 300 methane, 1725 water, and 300 
> > > methane, forming two interfaces parallel to the xy-plane. Now, the 
> > > accurate average-total-pressure is obtained from a short run (0.2 ns) 
> > > with the default tau_p (1 ps).
> > 
> > Please be careful when you use this kind of pressure coupling, you may
> > get the right pressure but you box might keep growing in one direction
> > forever. See bugzilla 165. Actually I'm pretty sure it will.
> > Unfortunately we don't really understand what is going on here.
> > > 
> > > 
> > > 
> > > Thank you for your kind replies and useful clues.
> > > 
> > > Guang-Jun
> > > 
> > > ------------------------------------------------------------------------
> > > From: gmx3 at hotmail.com
> > > To: gmx-users at gromacs.org
> > > Subject: RE: [gmx-users] Cannot obtain the expected pressure using the 
> > > Parrinello-Rahman coupling in a gas-liquid system
> > > Date: Sat, 28 Feb 2009 15:00:50 +0100
> > > 
> > > Hi,
> > > 
> > > Is 327 bar the averge total pressure or one the of components of the 
> > > pressure tensor?
> > > You will have a surface tension acting in the system causing a 
> > > difference in the different components.
> > > 
> > > Also it is still not completely clear to me how long you equilibrate and 
> > > average.
> > > Also the results will depend very much on the size of the system.
> > > In small systems the pressure fluctuations are enormous.
> > > With Berendsen these fluctuations will be surpressed, with PR not.
> > > 
> > > With PR I would use a tau_p of around 10 ps.
> > > You might need to average the pressure over several (tens of?) ns (after 
> > > several ns of equilibration)
> > > to obtain a good average.
> > > 
> > > Berk
> > > 
> > > ------------------------------------------------------------------------
> > > From: guogj at hotmail.com
> > > To: gmx-users at gromacs.org
> > > Subject: RE: [gmx-users] Cannot obtain the expected pressure using the 
> > > Parrinello-Rahman coupling in a gas-liquid system
> > > Date: Sat, 28 Feb 2009 13:51:15 +0000
> > > 
> > > Hi, Justin,
> > > 
> > > Thanks for your rapid reply. Let me decribes the question in more details.
> > > First ,two gaseous mathane systems and one liquid water system are 
> > > equilibrated at 300 bar and 250 K in advance. Then, the gas systems are 
> > > put at the both sides of liquid. The combined system is performed for 
> > > 3ns with the Parrinello-Rahman barostat, which produces a average 
> > > pressure of 327 bar. I am strange to the value and several tests are 
> > > run, mentioned previously. All these test runs take the end gro file of 
> > > the 3ns-run as the beginning. When the berendsen barostat is used, 
> > > the pressure is OK. When the Parrinello-Rahman barostat is used, the 
> > > questionary pressure occurs again. Although I will try to make a long 
> > > run for equilibrium, I think the equilibrium has reached because the 
> > > ~330 bar is always obtained no matter how long simulations are sampled, 
> > > from 0.2 ns to 3 ns. The version of Gromacs I used is 4.0.4. By the way, 
> > > how long did you equilibrate your membrane system and how many atoms 
> > > in it? Thanks again.
> > > 
> > > Guang-Jun
> > > 
> > > 
> > > 
> > > > Date: Sat, 28 Feb 2009 07:43:29 -0500
> > > > From: jalemkul at vt.edu
> > > > To: gmx-users at gromacs.org
> > > > Subject: Re: [gmx-users] Cannot obtain the expected pressure using 
> > > the Parrinello-Rahman coupling in a gas-liquid system
> > > >
> > > >
> > > >
> > > > GuoGuangjun wrote:
> > > > > In fact, I once run the gas-liquid interface for 3 ns, the pressure is
> > > > > still as high as 327 bar.
> > > >
> > > > There are two possibilities in my mind:
> > > >
> > > > 1. 3 ns is still not long enough.
> > > > 2. Your gas phase is causing the problem. If the pressure is right 
> > > for water
> > > > alone, then the problem likely comes from the inclusion of your gas 
> > > phase and
> > > > whatever parameters you're using for whatever species you have in 
> > > this phase.
> > > > Examine your parameters and consider how they were derived and 
> > > whether or not
> > > > they are adequate.
> > > >
> > > > Also, what version of Gromacs are you using? There were some changes 
> > > made to
> > > > the Parrinello-Rahman barostat between 3.3.x and 4.0.x.
> > > >
> > > > -Justin
> > > >
> > > > > Guang-Jun
> > > > >
> > > > >
> > > > > > Date: Sat, 28 Feb 2009 07:19:30 -0500
> > > > > > From: jalemkul at vt.edu
> > > > > > To: gmx-users at gromacs.org
> > > > > > Subject: Re: [gmx-users] Cannot obtain the expected pressure using
> > > > > the Parrinello-Rahman coupling in a gas-liquid system
> > > > > >
> > > > > >
> > > > > >
> > > > > > GuoGuangjun wrote:
> > > > > > >
> > > > > > > Hi, All,
> > > > > > > I am simulating an interface system composed of methane gas and 
> > > liquid
> > > > > > > water in the NPT ensemble. The temperature is well controlled 
> > > by using
> > > > > > > either the Berendsen or the Nose-Hoover T-couplings. As for 
> > > pressure,
> > > > > > > the Berendsen P-coupling also works well. However, the
> > > > > Parrinello-Rahman
> > > > > > > P-coupling always produces a higher pressure than the expected. For
> > > > > > > example, I set ref_p=300 bar in the mdp file but obtain an average
> > > > > > > pressure as ~330 bar (over 0.5 ns). I test the tau_p in the range
> > > > > 0.1 ~
> > > > > > > 10 ps, the case does not change. When I test the sin! ! gle-phase
> > > > > system,
> > > > > > > i.e., pure water, the Parrinello-Rahman P-coupling can indeed 
> > > produce
> > > > > > > the expected pressure with the deviation less than 2 bar. What 
> > > is the
> > > > > > > matter in the two-phase system?
> > > > > > >
> > > > > >
> > > > > > When I've used the Parrinello-Rahman barostat for membrane systems,
> > > > > it works
> > > > > > just fine. Perhaps 500 ps is too short of a timeframe to arrive at
> > > > > the average.
> > > > > > Heterogeneous systems often take longer to equilibrate.
> > > > > >
> > > > > > -Justin
> > > > > >
> > > > > > > Thanks a lot.
> > > > > > > Guang-Jun
> > > > > > >
> > > > > > >
> > > > > 
> > > ------------------------------------------------------------------------
> > > > > > > [UTF-8?]СЂПЬЯТди MSN [UTF-8?]БЃЛЄЖмЃЌБЃеЯ MSN [UTF-8?
]АВШЋЮШЖЈЃЁ [UTF-8?]ЯждкОЭЯТдиЃЁ
> > > > > > > <http://im.live.cn/safe/>
> > > > > > >
> > > > > > >
> > > > > > >
> > > > > 
> > > ------------------------------------------------------------------------
> > > > > > >
> > > > > > > _______________________________________________
> > > > > > >! ! ; gmx-users mailing list gmx-users at gromacs.org
> > > > > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > > > > Please search the archive at http://www.gromacs.org/search before
> > > > > posting!
> > > > > > > Please don't post (un)subscribe requests to the list. Use the
> > > > > > > www interface or send it to gmx-users-request at gromacs.org.
> > > > > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > > > > >
> > > > > > --
> > > > > > ========================================
> > > > > >
> > > > > > Justin A. Lemkul
> > > > > > Graduate Research Assistant
> > > > > > Department of Biochemistry
> > > > > > Virginia Tech
> > > > > > Blacksburg, VA
> > > > > > jalemkul[at]vt.edu | (540) 231-9080
> > > > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > > > > >
> > > > > > ========================================
> > > > > > _______________________________________________
> > > > > > gmx-users mailing list gmx-users at gromacs.org
> > > > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > > > Please! ! search the archive at http://www.gromacs.org/search before
> > > > > posting!
> > > > > > Please don't post (un)subscribe requests to the list. Use the
> > > > > > www interface or send it to gmx-users-request at gromacs.org.
> > > > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > > > >
> > > > > 
> > > ------------------------------------------------------------------------
> > > > > [UTF-8?]ФуКЭФуЕФАЎШЫЖМШÐ
Й§ФФРяЃППьРДЮЂШэЕиЭ
МвЛЦ№ЛцжЦАЎЕФЕиЭМАЩЃЁ [UTF-8?]СЂМДВщПДЃЁ
> > > > > <http://ditu.live.com/?form=MICHAJ >
> > > >
> > > > --
> > > > ========================================
> > > >
> > > > Justin A. Lemkul
> > > > Graduate Research Assistant
> > > > Department of Biochemistry
> > > > Virginia Tech
> > > > Blacksburg, VA
> > > > jalemkul[at]vt.edu | (540) 231-9080
> > > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > > >
> > > > ========================================
> > > > _______________________________________________
> > > > gmx-users mailing list gmx-users at gromacs.org
> > > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > > Please search the archive at http://www.gromacs.org/search before 
> > > posting!
> > > > Please don't post (un)subscribe requests to the list. Use the
> > > > www interface or send it to gmx-users-request at gromacs.org.
> > > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> > > 
> > > ------------------------------------------------------------------------
> > > [UTF-8?]ФуКЭФуЕФАЎШЫЖМШÐ
Й§ФФРяЃППьРДЮЂШэЕиЭ
МвЛЦ№ЛцжЦАЎЕФЕиЭМАЩЃЁ [UTF-8?]СЂМДВщПДЃЁ 
> > > <http://ditu.live.com/?form=MICHAJ>
> > > ------------------------------------------------------------------------
> > > Express yourself instantly with MSN Messenger! MSN Messenger 
> > > <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/>
> > > ------------------------------------------------------------------------
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8?]СЂПЬЯТдиЃЁ 
> > > <http://im.live.cn/msn9/>
> > > 
> > > 
> > > ------------------------------------------------------------------------
> > > 
> > > _______________________________________________
> > > gmx-users mailing list gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please search the archive at http://www.gromacs.org/search before posting!
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> > > www interface or send it to gmx-users-request at gromacs.org.
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> > 
> > 
> > -- 
> > David van der Spoel, Ph.D., Professor of Biology
> > Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> > spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
> > _______________________________________________
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