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

[Justin A. Lemkul]

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?
> 

 From the documentation, it might seem that way.  But -deffnm seems to only act 
on output files, so -s is taking the default, topol.tpr.  You need to explicitly 
tell mdrun that your input is em.tpr.

-Justin

> -------------------------------------------------------
> 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
> 
> 
> 
> 
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> 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 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 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)
>>
>>
>>
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> 

-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================