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  "GROMOS87" refers to the (outdated!)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

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

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

==================================================
--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a 
mail to gmx-users-requ...@gromacs.org.

Reply via email to