On 12/4/13 11:03 AM, Mahboobeh Eslami wrote:
dear Justin
thanks for reply
I don't find tutorial for ATB and I don't know that which files are used for itp

It works much like PRODRG.  You can upload coordinates or draw the molecule.

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?

It seems that if you want to upload your own molecule, the force field is 53A6. It is trivial to interconvert between Gromos parameter sets, though, by simple modifications. Of course, you can always derive the parameters from scratch yourself ;)

-Justin



On Wednesday, December 4, 2013 7:07 PM, Justin Lemkul <jalem...@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  "GROMOS87" refers to the (outdated!)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


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

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 <mailto:jalem...@outerbanks.umaryland.edu> |
(410) 706-7441


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



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

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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