[gmx-users] Cannot find position restraint file restraint.gro

[Justin Lemkul]

On 1/22/18 8:48 AM, Sailesh Bataju wrote:
>> The error message tells you exactly what to do (it's probably one of the
>> most verbose error messages I've ever seen). The -r argument is now
>> required.
>> -Justin
> I'm sorry to say sir, I didn't find restraint.gro file if i've to use
> -r option. I have no idea which .gro file is to be used.

Quoting the error message:

"although you can still use the same file as you specify for the -c option."

Position restraints require reference positions to determine the origin 
of the biasing potential. In past versions, these were just read from 
the file passed to -c unless the user provided a different file to -r. 
Now, the use of -r with some coordinate file is required to avoid making 
mistakes.

-Justin

> Thank you very much for your help.
>
>
> On Mon, Jan 22, 2018 at 1:05 PM, Sailesh Bataju <thelaven at gmail.com> wrote:
>
>> Hi,
>>
>> I have been trying to simulate isobutane in urea as a solvent. I have made
>> myself urea.itp and urea.gro file for charmm36 forcefield under
>> equilibrating at certain temperature and pressure. First nvt followed by
>> npt I got error like this while equilibriating.
>>
>> Program:     gmx grompp, version 2018
>> Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2008)
>>
>> Fatal error:
>> Cannot find position restraint file restraint.gro (option -r).
>>  From GROMACS-2018, you need to specify the position restraint coordinate
>> files
>> explicitly to avoid mistakes, although you can still use the same file as
>> you
>> specify for the -c option.
>>
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>>
>> Despite of this error, I continue comment define= -DPOSRE in .mdp file.
>> Then the simulation run smoothly without any error.
>>
>> After urea has been equilibriated in  a box under certain temperature and
>> pressure . Now i've to put isobutane molecule in it. There has been no
>> error till energy minimization. But when i've to equilibriate in nvt, I got
>> error like this.
>>
>> GROMACS:      gmx grompp, version 2018
>> Executable:   /usr/local/gromacs/bin/gmx
>> Data prefix:  /usr/local/gromacs
>> Working dir:  /home/sailesh/Documents/Thesis/urea_1000
>> Command line:
>>    gmx grompp -f nvt_urea.mdp -c em_urea.gro -p topol.top -o nvt_urea.tpr
>>
>> Ignoring obsolete mdp entry 'title'
>> Generated 85052 of the 85078 non-bonded parameter combinations
>> Generating 1-4 interactions: fudge = 1
>> Generated 55198 of the 85078 1-4 parameter combinations
>> Excluding 3 bonded neighbours molecule type 'Alkane_chain_A'
>> Excluding 3 bonded neighbours molecule type 'Urea'
>> Velocities were taken from a Maxwell distribution at 298 K
>> Removing all charge groups because cutoff-scheme=Verlet
>>
>> -------------------------------------------------------
>> Program:     gmx grompp, version 2018
>> Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2008)
>>
>> Fatal error:
>> Cannot find position restraint file restraint.gro (option -r).
>>  From GROMACS-2018, you need to specify the position restraint coordinate
>> files
>> explicitly to avoid mistakes, although you can still use the same file as
>> you
>> specify for the -c option.
>>
>> For more information and tips for troubleshooting, please check the GROMACS
>> website at http://www.gromacs.org/Documentation/Errors
>> -------------------------------------------------------
>> turning all bonds into constraints...
>> turning all bonds into constraints...
>>
>> This is my end part of topol.top file for isobutane in urea.
>>
>> ; Include Position restraint file
>> #ifdef POSRES
>> #include "posre.itp"
>> #endif
>>
>> ; Include urea topology
>> #include "charmm36.ff/urea.itp"
>> #ifdef POSRES
>> #include "posre_urea.itp"
>> #endif
>>
>> ; Include topology for ions
>> #include "charmm36.ff/ions.itp"
>>
>> [ system ]
>> ; Name
>> Isobutane in Urea
>>
>> [ molecules ]
>> ; Compound        #mols
>> Alkane_chain_A      2
>> Urea 841­
>>
>> Any idea to solve this problem.
>>
>> Thank you for your time and effort.
>>
>> Sailesh Bataju.
>>
>>
>

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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