[gmx-users] Problem with editconf

[Justin Lemkul]

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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