Hi Dear David,
Thank you for such a detailed reply. I really appreciate your help and patience, It really helps a lot. You asked me, what I really want to do? 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. For this purpose, you suggested me that either I parameterize active site water molecules with different name like WAR rather than WAT or I just let tleap treat all waters (crysatl water + solvate box water) the way it wants to treat waters. If my understanding is wrong, kindly correct me.
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
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|
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
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Received on Fri Jan 22 2016 - 07:00:03 PST
