mohsen ramezanpour wrote:
Thanks for your guidance.
I looked that file,But I think the name of functional groups are
different in .rtp file because I can't find no one of them in this file.
Functional group names are not in the .rtp files. You locate applicable
functional groups by knowing the residues in which they occur.
please let me know how can I know the correct name f or functional groups
for example:HYDROXYL,CARBOXYL,HALO,AMINO and ...
All of these except halogens exist in common amino acids. If you have many
non-standard groups (i.e. those that don't typically occur in biomolecules),
then perhaps your choice of force field was a poor one. As Mark said, don't
presuppose the solution.
-Justin
Thanks in advance for your help
On Mon, Jan 24, 2011 at 4:01 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
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.
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.
Please keep your story consistent. In the last message, you said
you wanted to work completely within 53A6, so I advised you on how
to do that, now you say that you're trying to work completely within
43A1.
Unfortunately I can't obtain these parameter.
You certainly do have these parameters. 43A1 is part of the Gromacs
installation; in the .rtp file you'll find all of the functional
groups that were derived in 43A1, as applied to amino acids and a
few other groups.
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!
My paper that you said you read has discussion and recommendations
on this point. But be very clear: none of the QM methods we tested
were able to reproduce the charges that are assigned to known
functional groups since the Gromos parameterization methodology
calls for "empirical refinement." Thus, manual modification and
thorough validation are always necessary.
-Justin
Thanks in advance
On Sat, Jan 22, 2011 at 8:03 PM, Justin A. Lemkul
<jalem...@vt.edu <mailto:jalem...@vt.edu>
<mailto: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>>
<mailto: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
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ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
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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> <http://vt.edu> | (540)
231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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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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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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