[gmx-users] GMX to remove clashes?

[Liu, Liang]

Thanks.

Do you know how to use a new force field, not amber or charm, but a force
field built by someone else, and it's already in Gromacs format (tons of
xvg file, right?)

On Mon, Nov 14, 2011 at 4:13 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Liu, Liang wrote:
>
>> This is a "reasonable" answer :)
>>
>> Thanks for that, and I just tried Gromacs for minimization, and looks the
>> final structure does not have clashes anymore, and also are very close to
>> the initial structure.
>>
>> Another question is if there is a way to add ions automatically, meaning
>> no need to check the "NOTE" of "System has non-zero total charge" in the
>> output of grompp command? And also update the topology file automatically
>> too?
>>
>>
> That depends on the system.  For a simple solute in water, the running
> total charge of the solute is recorded in the qtot column of the .top file.
>  If you have a complex system with lots of charged things, no, there is no
> convenient way to get the charge aside from calculating it by hand or
> reading the grompp output.
>
> The topology can be modified automatically by genion after ions are added
> by using the -p flag.
>
> -Justin
>
>  On Mon, Nov 14, 2011 at 3:49 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>>
>>
>>
>>    Liu, Liang wrote:
>>
>>        Hi, all,
>>        I am wondering if Gromacs can do the following work?
>>
>>        Assuming I have a pdb file of an RNA molecule. Some atoms may be
>>        too close or even overlap, I am wondering if Gromacs can move
>>        the atoms to reasonable positions and remove the bad contacts?
>>        The final structure is supposed to be the "most" stable
>>        structure with minimal energy. I know AMBER minimization can do
>>        this work, and I am wondering if Gromacs can do the same?
>>
>>
>>    Gromacs is perfectly capable of energy minimization.  Whether or not
>>    minimization succeeds and gives a reasonable output is mostly
>>    dependent upon the feasibility of the starting structure.  If the
>>    minimization crashes, it's not Gromacs' fault ;)
>>
>>    -Justin
>>
>>    --     ==============================**__==========
>>
>>
>>    Justin A. Lemkul
>>    Ph.D. Candidate
>>    ICTAS Doctoral Scholar
>>    MILES-IGERT Trainee
>>    Department of Biochemistry
>>    Virginia Tech
>>    Blacksburg, VA
>>    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>    <tel:%28540%29%20231-9080>
>>    http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
>>    <http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>> >
>>
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>>
>>
>> --
>> Best,
>> Liang Liu
>>
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
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-- 
Best,
Liang Liu
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