[gmx-users] GMX to remove clashes?
Justin A. Lemkul
jalemkul at vt.edu
Mon Nov 14 23:19:34 CET 2011
Liu, Liang wrote:
> 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?)
>
Force fields are not in .xvg format, unless you're talking about using tabulated
potentials. In either case, please see the manual and the help information on
gromacs.org, and start a new thread with more information to change topics if
you have further questions.
-Justin
> On Mon, Nov 14, 2011 at 4:13 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto: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>
> <mailto: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> <http://vt.edu> | (540)
> 231-9080 <tel:%28540%29%20231-9080>
> <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 <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
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