Re: [AMBER] Atom type error

From: Vikas Sharma <vs_vikassharma.yahoo.co.in>
Date: Tue, 21 Apr 2009 07:55:24 +0100

Hi Ross, I am working on MM PBSA.. As per the tutorial I am minimizing,heating & equilibrating the protein -ligand complex... I used a step size of 0.001 ps for heating.... will it be ok for me to use a step size of 0.002 ps for equilibration and production MD coz running with 0.001ps is taking a lot of time... I have applied SHAKE Thanks ________________________________ From: Ross Walker <ross.rosswalker.co.uk> To: AMBER Mailing List <amber.ambermd.org> Sent: Monday, 20 April, 2009 2:53:38 AM Subject: RE: [AMBER] Atom type error Hi Vikas, > Now after loading the protein i wanted to solvate it, so i found out > the charge in xleap using 'charge ' command..it comes out to be : > > 'total perturbed charge = 9.000100 > 'total unperturbed charge = 9.000100' > > i added 9 Cl- bt the charge still remains 0.000100... > what should i do now... This is an acceptable amount since most of the charges are only defined to 4 decimal places anyway. Sander / PMEMD will take care of this residual charge when it runs. All the best Ross /\ \/ |\oss Walker | Assistant Research Professor | | San Diego Supercomputer Center | | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk | | http://www.rosswalker.co.uk | PGP Key available on request | Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues.  _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber Now surf faster and smarter ! Check out the new Firefox 3 - Yahoo! Edition http://downloads.yahoo.com/in/firefox/
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Received on Wed May 20 2009 - 11:56:35 PDT
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