[gmx-users] GMX to remove clashes?

Liu, Liang liu4gre at gmail.com
Mon Nov 14 23:11:46 CET 2011

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

On Mon, Nov 14, 2011 at 3:49 PM, Justin A. Lemkul <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
> Department of Biochemistry
> Virginia Tech
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> 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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Liang Liu
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