[gmx-users] Problem with editconf

abhishek khetan askhetan at gmail.com
Mon Jan 4 18:44:22 CET 2016


I checked it. the pdb files are totally wrong but using vmd when i look at
the gro files, all is well.

On Mon, Dec 28, 2015 at 9:53 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/28/15 3:49 PM, abhishek khetan wrote:
>
>> Thanks for your reply again. Yes, it seems indeed a particularly difficult
>> task. I tried to used the command :
>>
>> $ gmx_mpi insert-molecules -ci DME_new.pdb -nmol 216 -box 4.0 4.0 4.0 -o
>> dme_box.pdb > logfile
>>
>> When I look at the file dme_box.pdb, its nothing but the whole thing in a
>> 4x4x4 box and the moecules are pulverised, broken and atoms randomly
>> thrown
>> off (of course i do check before if the input DME_new.pdb is okay or not).
>> Could you please suggest me how to start on this altogether? any
>> tutorials?. The ones on this page already start off at an advanced place
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/
>> for
>> me to be able to figure out what i am doing wrong.
>>
>>
> The command shown works fine for me, using the DME_new.txt you originally
> posted as the input coordinates.
>
> -Justin
>
>
>
>> On Sat, Dec 26, 2015 at 4:06 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 12/26/15 5:20 AM, abhishek khetan wrote:
>>>
>>> Thanks for your reply. Any idea what is the source of this error then ?
>>>>
>>>>
>>> Again, there is no error.
>>>
>>> This should have been relatively simple to do but I don't know what I'm
>>>
>>>> doing wrong. I've tried to run it with the minimum number of arguments
>>>> as
>>>> well. Have specified the -box as 1 but to no avail. Its always showing
>>>> volume as zero.
>>>>
>>>>
>>>> This is not the way to write boxes of solvents.  You can't use editconf
>>> to
>>> scale the density of one molecule into an actual liquid.  What you want
>>> is
>>> gmx insert-molecules to build a box of sufficient size to carry out the
>>> simulation.  The density is then a result of the force field parameters
>>> for
>>> the liquid.  If the parameters are good, so too should be the
>>> condensed-phase properties (not necessarily a simple task).
>>>
>>> -Justin
>>>
>>>
>>> Best,
>>>
>>>> askhetan
>>>>
>>>> On Sat, Dec 26, 2015 at 2:23 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>>
>>>>
>>>>
>>>>> On 12/25/15 7:42 PM, abhishek khetan wrote:
>>>>>
>>>>> Hello everyone,
>>>>>
>>>>>>
>>>>>> I am a new user and am trying to generate a solventbox for non-water
>>>>>> solvation. the solvent in this case is dimethoxyethane(DME), the *.pdb
>>>>>> for
>>>>>> which i generated using the software openbabel, because i had only its
>>>>>> xyz
>>>>>> format at hand. Now using this generated pdb i am giving the command
>>>>>> on
>>>>>> my
>>>>>> cluster which has gromacs/5.0.4 installled
>>>>>> $ gmx_mpi editconf -f DME_new.pdb -bt o -d 0.5 -density 868.3
>>>>>>
>>>>>> for which the error file says:
>>>>>> --------------------
>>>>>> WARNING: all CONECT records are ignored
>>>>>> Volume  of input 0 (nm^3)
>>>>>> Mass    of input 90.1206 (a.m.u.)
>>>>>> Density of input inf (g/l)
>>>>>> --------------------
>>>>>>
>>>>>>
>>>>>> And the output is:
>>>>>> --------------------
>>>>>> Read 16 atoms
>>>>>> No velocities found
>>>>>>        system size :  0.454 0.618 0.178 (nm)
>>>>>>        diameter    :  0.756               (nm)
>>>>>>        center      :  0.000  0.000  0.000 (nm)
>>>>>>        box vectors :  0.000  0.000  0.000 (nm)
>>>>>>        box angles  :   0.00   0.00   0.00 (degrees)
>>>>>>        box volume  :   0.00               (nm^3)
>>>>>>
>>>>>> WARNING: Masses and atomic (Van der Waals) radii will be guessed
>>>>>>             based on residue and atom names, since they could not be
>>>>>>             definitively assigned from the information in your input
>>>>>>             files. These guessed numbers might deviate from the mass
>>>>>>             and radius of the atom type. Please check the output
>>>>>>             files if necessary.
>>>>>> --------------------
>>>>>>
>>>>>> Clearly, something is wrong with the input DME_new.pdb file because
>>>>>> the
>>>>>> CONECT are all ignored. I have attached the contents of the pdb file
>>>>>> in
>>>>>> the
>>>>>> text file.
>>>>>>
>>>>>> Iwant to do simulations for quite a few solvents and solutes for which
>>>>>> the
>>>>>> pdb files may not be readily available. Could you please suggest a
>>>>>> consistent way of doing this/getting around this error ?
>>>>>>
>>>>>>
>>>>>> It's not an error.  CONECT records are ignored by all GROMACS
>>>>>> programs;
>>>>>>
>>>>> bonded information is always read from the topology, where applicable.
>>>>> It's not relevant when running editconf.
>>>>>
>>>>> -Justin
>>>>>
>>>>> --
>>>>> ==================================================
>>>>>
>>>>> Justin A. Lemkul, Ph.D.
>>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>>>
>>>>> Department of Pharmaceutical Sciences
>>>>> School of Pharmacy
>>>>> Health Sciences Facility II, Room 629
>>>>> University of Maryland, Baltimore
>>>>> 20 Penn St.
>>>>> Baltimore, MD 21201
>>>>>
>>>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>>>> http://mackerell.umaryland.edu/~jalemkul
>>>>>
>>>>> ==================================================
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
>>>>> * Please search the archive at
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>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>>>
>>>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
>>> Department of Pharmaceutical Sciences
>>> School of Pharmacy
>>> Health Sciences Facility II, Room 629
>>> University of Maryland, Baltimore
>>> 20 Penn St.
>>> Baltimore, MD 21201
>>>
>>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>>> http://mackerell.umaryland.edu/~jalemkul
>>>
>>> ==================================================
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
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>>>
>>>
>>
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
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> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
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>



-- 
|| radhe radhe ||

abhishek


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