[gmx-users] GMX to remove clashes?

[Justin A. Lemkul]

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://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

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