Re: CHARMM HELP NEEDED!!!

Hi all
 I just want to let everyone know that I have solved my own problem.
 What happened was that I was translating half of a 74.5848 A box of
 water 24.8616 A, instead of translating it 74.5848 A.  Thus, this  leads
 to
 bad contacts, and bad energy.
 I want to thank everyone that offered suggestions to me.
 Cheers,
 Richard
 "Dr. Richard L. Wood" wrote:
 > Hi all
 >
 > I have what I think is a very strange problem.
 >
 > I'm curently using a "big" version of CHARMm, one that will
 handle
 > 60,000+ atoms.
 > I have built a system that consists of a glycosylated peptide having 27
 > amino acids and
 > 21 mannoses.  The system is solvated with 14,375 TIP3P waters, giving a
 > total of 43,915
 > atoms.  When I try and calculate the energy of the system with all the
 > waters present, the
 > energy goes through the roof; that is to say, I get stars instead of
 > numbers for the energy.
 > However, if I change the number of waters in the lines
 >
 > READ SEQUENCE TIP3 8844
 > GENERATE WAT NOANGLE NODIHE
 >
 > READ SEQUENCE TIP3 5531
 > GENERATE WAT2 NOANGLE NODIHE
 >
 > to this:
 >
 > READ SEQUENCE TIP3 5700
 > GENERATE WAT NOANGLE NODIHE
 >
 > CHARMm is able to read the structure in and calculate its energy.
 >
 > The other way, with 14,375 waters defined in the input file, it will
 > read the structure in,
 > but claculates the energy as *********.  I don't want to go with only
 > 5700 waters as my peptide
 > won't be completely solvated.  With the 14,375 waters, I have a shell
 > around the peptide about 18 A
 > thick.
 >
 > Obviously, I'm under the 60,000 atom limit, but I'm over some other
 > limit that I'm not aware of.
 > Has anyone encountered this problem before and how is it handled?
 >
 > Thank you in advance.
 >
 > Richard
 >
 > --
 > Richard L. Wood, Ph. D.
 > Physical/Computational Chemist
 > Post-doctoral Associate
 > Department of Food Science
 > 120 Stocking Hall
 > Cornell University, Ithaca, NY 14853
 --
 Richard L. Wood, Ph. D.
 Physical/Computational Chemist
 Post-doctoral Associate
 Department of Food Science
 120 Stocking Hall
 Cornell University, Ithaca, NY 14853