[gmx-users] Problem with editconf

[Justin Lemkul]

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
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> 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

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