shahrbanoo karbalaee wrote:
Dear justin
as your telling I have two way for my problem:
1-choose force field that is compatible to TFE(with 7 atom) that I
used another force field.I made tfe.pdb (with 7 atom) and choose
gromos 96 but I got error that dont found HO atom.
Are you trying to create the topology with pdb2gmx? If so, which parameter set
of Gromos96? There are several, you know. You have to give background (and
again, as always, commands) to get information. No one on this list can get
inside your head! If you're using pdb2gmx, it should work, as there are TFE
entries within Gromos96 (at least, the 53a5 and 53a6 parameter sets), if you use
the right atom nomenclature. Check the .rtp file.
2)another way,I must itp file for tfe with opls forcefield.IF it is
please advise me.
You can certainly make one. Have a look at:
http://wiki.gromacs.org/index.php/Parameterization
The bottom line is this: Do not choose a force field simply because it may make
your life easier in automating some steps of system preparation. Choose a force
field that will accurately simulate the properties you are interested in, using
the best model. I don't know whether Gromos96 or OPLS-AA will be better for
you, and maybe (when using an appropriate model) they will give equivalent
results. The choice is yours, and will require lots of background reading and
careful consideration.
-Justin
first I must make topology file with pd2gmx for tfe and make tfe.itp
.and insert in top folder?
best and appreciate you very much
sh-karbalaee
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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