[gmx-users] force field for prodrg server

[Mahboobeh Eslami]

dear Justin
thanks for reply
I don't find tutorial for ATB and I don't know that which files are used for itp and gro files from ATB result, Moreover in gromacs site is mentioned  that PRODRG is used  for GROMOS96 force field, 43A1. can I use ATB for 43A1 force field?



On Wednesday, December 4, 2013 7:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
  


On 12/4/13 10:24 AM, Mahboobeh Eslami wrote:
> hi dear Justin
>
> You've written the following context in your tutorial:
>
>
> Force field (GROMOS96.1/GROMOS87): "GROMOS96.1" refers to the first version of the GROMOS96 force field, 43A1.  "GROMOS87" refers to the (outdated!) GROMOS87 force field.  Choose "GROMOS96.1" to get 43A1 parameters for our ligand
>
> but I don't see the option for Select the force field in PRODRG server

PRODRG is now hosted by a company, so I don't know what sorts of changes they 
have introduced.  There is no more force field selection, so it's a black box, I 
suppose.  Given that you probably have to re-write the topology anyway, it 
probably doesn't matter much except for a few atom types that may be different 
between the force fields.

ATB is probably a better option; I think its output is generally much more 
reliable than PRODRG.  I'll probably revise the tutorial at some point, but the 
use of PRODRG to get a flawed topology is a good teaching tool.


-Justin

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Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

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