[gmx-users] PRODRG server
Justin A. Lemkul
jalemkul at vt.edu
Mon Jan 24 15:47:34 CET 2011
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 <jalemkul at vt.edu
> <mailto:jalemkul at 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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>
> <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> <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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--
========================================
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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