[gmx-users] genbox command in gromacs-5.0.1

[Kalyanashis Jana]

Thank you very much Justin. I need the solvated box. I have used "gmx
solvate -cp *.pdb -cs tip4p.gro -p topol.top -o *.pdb" . It has
successfully generated the solvent box.
Thank you,
Kalyanashis Jana


On Wed, Apr 8, 2015 at 6:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/8/15 8:38 AM, Kalyanashis Jana wrote:
>
>> Dear all,
>> I have installed gromacs-5.0.1 version successfully but when I have run
>> the
>> genbox command, it has shown that "This tool has been removed from Gromacs
>> 5.0. Please see
>>    http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0
>> for ideas how to perform the same tasks with the new tools."
>>
>>
>> In gromacs site, it is written that
>> genbox
>>
>> This tool has been split to gmx solvate and gmx insert-molecules.
>>
>> Can anyone please help me?
>>
>>
> With what task?  genbox has been split based on two core functions:
> solvation and insertion of molecules.  Start with "gmx help solvate" and
> "gmx help insert-molecules" to see how to use each.
>
> -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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-- 
Kalyanashis Jana
email: kalyan.chem.in at gmail.com