[gmx-users] PRODRG server
Justin A. Lemkul
jalemkul at vt.edu
Mon Jan 24 13:31:40 CET 2011
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>> 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>>> 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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--
========================================
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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