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 <jalem...@vt.edu
<mailto:jalem...@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
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@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
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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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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>
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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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