[gmx-users] Problem with editconf

[abhishek khetan]

Thanks for your reply. Any idea what is the source of this error then ?
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.

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.
>