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  "GROMOS87" refers to the (outdated!)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 A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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