[gmx-users] Problem with editconf
Justin Lemkul
jalemkul at vt.edu
Mon Dec 28 21:53:36 CET 2015
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
>>>>
>>>> ==================================================
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>>>> Gromacs Users mailing list
>>>>
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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
>>
>> ==================================================
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>> 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
==================================================
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