On Fri, Jan 22, 2016 at 7:29 AM, Saman Yousuf ali
<saman.yousufali64.yahoo.com> wrote:
> Actually the reason of making active site water molecules unique is just to trace them easily after MD, as you said that the water molecules exchange during simulation.
If all you want to do is track an individual water molecule you don't
need any special parameters. Just note the residue number and use that
to track it.
-Dan
>
> Thanks alot
> Best Regards, Saman Yousuf AliJunior Research Fellow,
> | Lab No. P-133, Computational Chemistry Laboratory
> Dr. Panjwani Center for Molecular Medicine & Drug Research,
> International Center for Chemical & Biological Sciences,
> University of Karachi – 75270.Karachi-Pakistan.
>
> Contact No:
> Office (92-21) 111222292 (Ext 309)
> Email ID: saman.yousufali64.yahoo.com
> saman.ali.iccs.edu
>
> |
>
>
>
> On Friday, January 22, 2016 5:13 AM, David A Case <david.case.rutgers.edu> wrote:
>
>
> On Fri, Jan 22, 2016, Saman Yousuf ali wrote:
>>
>> > Error: A residue defined as a "fast 3-point water"
>> is not defined by a triangle of three bonds.
>> Residue 539 contains 2 bonds.I
>> have also prepared water prepin and frcmod for making active site water
>> molecule different from TIP3P water box molecules. Parameter files for
>> crystal water are attached below,
>
> First, be sure that you really want the crystal waters to have a different
> force field than other waters. I would think that this would be hard to
> justify, since waters will exchange during a simulation. But I'll leave that
> decision to you--you may well have considerations that I don't know about.
>
> TIP3P waters are implemented as rigid bodies in Amber by defining three bonds,
> including an H-H bond. If you want to have (e.g.) a flexible water, that
> doesn't have the third bond, the simplest thing is to give it a different
> residue name: don't use "WAT". Amber uses residue names to create all kinds
> of data structures, and if you want the crystal waters to be different than
> the other waters, you have to give your special ones a new 3-letter name.
>
> ...hope this helps...dac
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 22 2016 - 07:30:04 PST
