On 24/01/2011 10:06 PM, mohsen ramezanpour wrote:
Dear Dr.justin
Actually by doing this we are using two different force fields in one
simulation.
I had done it before and the result was that I discussed before in
gmx-users(LINCS Error,Exploding system,Bad contacts between atoms)
Then,this approch seems to doesn't work about my system.
Sounds like you've re-learned the lessons here:
http://www.gromacs.org/Documentation/How-tos/Parameterization
Then I want to find charges and charge groups for gromos 43A1 and
replace them for my drug(to edit PRODRG file manually) and work
totally in gromos 43A1.
Unfortunately I can't obtain these parameter.
Please let me have if you have it.
Can I use some Ab Initio software for determining partial charges of
my drug?
for example ABINIT or Gaussian!
You should choose a force field based on the likelihood of being able to
successfully make your observations. You want one that has a record of
useful performance on similar systems, for which you can develop
reasonably reliable parameters readily, test them suitably, and run
simulations smoothly. Don't presuppose the form of the solution.
Mark
Thanks in advance
On Sat, Jan 22, 2011 at 8:03 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
mohsen ramezanpour wrote:
Ok
then,I can use PRODRG server to generate .top and .gro files
for drug.
since it's reported charges are not very accurate ,we can
replace all charges completely with them in 53A6(if was present).
But it means we are working in 53A6 force field.
then,we must generate .top and .gro files for our protein with
53A6 too.
and work completely with 53A6.
Am i right?
thanks in advance
That sounds like a reasonable approach. Be sure to validate the
drug topology. In my experience, this procedure is pretty good,
but you always have to convince reviewers...
-Justin
On Sat, Jan 22, 2011 at 4:43 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:
mohsen ramezanpour wrote:
Dear Justin
I read your articles about PRODRG server,they were very
useful.
But I have a question:
are charges of functional groups and generally other
atom groups
the same in all force fields?
Because you have modified charges of your molecules by
Gromos96
53A6 while prodrg server is generating topology files
in 43A1.
I want to know can I replace charges from gromos 53A6
or other
forcefields?
thanks in advance
Charges are not the same between force fields. We did our
study
with 43A1 since that is what PRODRG purports to produce. I
would
say that our recommendations carry to other Gromos force
fields, as
well, but don't take charges from 43A1 and apply them to
53A6. Be
consistent within the force field.
The atom types produced by PRODRG are largely shared
between 43A1
and 53A6, so if you *completely* replace all charges with
those from
53A6, you should have a topology that is compatible with 53A6.
-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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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