From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Wed Mar 11 2009 - 18:00:21 CDT
It sounds like you should probably consider using TclForces (specifically TclBC Forces) to establish a slab volume between the proteins such that any water (with coordinates inside the defined rectangle) is driven out of the defined rectangle. Just turning off the electrostatics will not resolve the vdW interactions and simply making all the waters "disappear" via alchemical FEP or similar approaches will be more work than either a) learning and writing a short TclForces script or b) just loading the system in vmd and writing a psfgen script to loop over all atoms and delete those between the proteins then write a new psf/pdb. However solution b, as well as the alchemical and alchemical-like solutions, will not prevent any waters from entering the "vacuum" created by deleting interfacial waters between the two proteins. A tutorial for Tcl Forces (and TclBC) can be found at:
http://www.ks.uiuc.edu/Training/Tutorials/science/forces/forces-tutorial-html
and necessary tutorial files at:
http://www.ks.uiuc.edu/Training/Tutorials/science/forces/forces-tutorial-files.tar.gz
C.
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078 govardhan reddy <greddy1_at_umd.edu> writes: > Date: Wed, 11 Mar 2009 16:57:33 -0400 > From: govardhan reddy <greddy1_at_umd.edu> > To: Chris Harrison <char_at_ks.uiuc.edu> > Cc: namd-l_at_ks.uiuc.edu > Subject: Re: namd-l: Selectively turning off electrostatic interactions > Return-Path: char_at_halifax.ks.uiuc.edu > Message-Id: <8389FF94-9A25-43B6-BFF7-A747D62E4A98_at_umd.edu> > X-Spam-Status: No, score=-2.5 required=5.0 tests=AWL,BAYES_00, > DNS_FROM_RFC_ABUSE autolearn=no version=3.1.7-0+tcb1 > > Hello Chris, > I have a layer of water trapped between two domains of the protein > preventing the collapse of the domains. I believe electrostatic > interactions between the protein and water are responsible for this > metastable state. I want to see whether the collapse of the domains will > accelerate or not if I switch off these interactions. > Thanks > G. Reddy > > > On Mar 11, 2009, at 4:28 PM, Chris Harrison wrote: > >> Greddy, >> >> Can you please explain why you want to do this, particularly with an >> entire protein? This will not provide an accurate free-energy of >> solvation which some people have naively suggested before. Leaving >> the vdW potentials in full effect without electrostatics will result >> in aberrant dynamics that will propagate through your system with time >> leading to large inaccuracies. If you're lucky, the simulation will >> simply crash with velocity exceptions after several timesteps. >> >> >> C. >> >> >> >> -- >> Chris Harrison, Ph.D. >> Theoretical and Computational Biophysics Group >> NIH Resource for Macromolecular Modeling and Bioinformatics >> Beckman Institute for Advanced Science and Technology >> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 >> >> char_at_ks.uiuc.edu Voice: 217-244-1733 >> http://www.ks.uiuc.edu/~char Fax: 217-244-6078 >> >> >> govardhan reddy <greddy1_at_umd.edu> writes: >>> Date: Wed, 11 Mar 2009 12:36:57 -0400 >>> From: govardhan reddy <greddy1_at_umd.edu> >>> To: namd-l_at_ks.uiuc.edu >>> Subject: namd-l: Selectively turning off electrostatic interactions >>> Return-Path: char_at_halifax.ks.uiuc.edu >>> Message-Id: <69F5EBCD-A786-490B-8769-DFDB87778E30_at_umd.edu> >>> X-Spam-Status: No, score=-2.6 required=5.0 tests=AWL,BAYES_00 >>> autolearn=unavailable version=3.1.7-0+tcb1 >>> >>> Hello all, >>> >>> I have a protein solvated in water. I just want to turn off protein- >>> water electrostatic interactions but keep the protein-protein and >>> water-water electrostatic interactions intact. If anybody has >>> performed >>> such kind of calculations in NAMD or in any other package before, I >>> will >>> be grateful if you can provide me any input. >>> >>> Thanks >>> Greddy >>> >> > > *************************************************** > Govardhan Reddy > Research Associate > Institute for Physical Science and Technology > University of Maryland-College Park > College Park, MD - 20742 > Phone: +1-301-405-4822 > Fax: +1-301-314-9404 >
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