[gmx-users] PRODRG server

[Justin A. Lemkul]

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>> 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> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> 
>     ========================================
>     -- 
>     gmx-users mailing list    gmx-users at gromacs.org
>     <mailto:gmx-users at gromacs.org>
>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>     Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>     Please don't post (un)subscribe requests to the list. Use the www
>     interface or send it to gmx-users-request at gromacs.org
>     <mailto:gmx-users-request at gromacs.org>.
>     Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> 

-- 
========================================

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

========================================