[gmx-users] PRODRG server

[Mark Abraham]

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 <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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