AMBER Archive (2003)

Subject: AMBER: Fwd: Minimizing after solvation

From: Angela Pantelogianis (ap924_at_nyu.edu)
Date: Fri Jul 18 2003 - 17:34:30 CDT

attached mail follows:

Hello,

I am running minimization on an RB69-PhIP system. I have already added Na+ ions and ran one minimization holding the main chain atoms still. I created a pdb file from the restrt file after minimization and reloaded it into tleap. I then solvated the system by using

solvateBox WATBOX216 10.0

Everything went fine, and I then saved the new coordinates and parameters under .prmtop and .inpcrd

The files saved with no errors.

My next step was to minimized the system by holding the system still and equilibrating the solvent and ions. Here is my input file for sander_classic:

Minimization of Na+ and added solvent water holding all other atoms still
 &cntrl
  ntpr=1,
  ntf=1, idiel=0, dielc=1, scnb=2, scee=1.2, cut=10.0
  imin=1, maxcyc=5000, ncyc=50, ntmin=1,
  ntr=1,
 &end
 Group input for restraining DNA,Mg2+,Protein
 100
 RES 1 937
 END
 Group input for restraining crystal water
 100
 RES 969 1315
 END
END

I then got the error:

   1. RESOURCE USE:

 NATOM = 128941 NTYPES = 22 NBONH = 120848 MBONA = 8324
 NTHETH = 17465 MTHETA = 11398 NPHIH = 32724 MPHIA = 21085
 NHPARM = 0 NPARM = 0 NNB = 237905 NRES = 38701
 NBONA = 8324 NTHETA = 11398 NPHIA = 21085 NUMBND = 75
 NUMANG = 176 NPTRA = 68 NATYP = 41 NPHB = 1
 IFBOX = 1 NMXRS = 60 IFCAP = 0

  ** failed to allocate pair array, bytes: -554087692

My second problem came when I tried to create a new pdb file with the added solvent included. It gave me the error:

  ATOMS DO NOT MATCH BETWEEN PARM AND MIN FILES

Any suggestions?

Thank you very much,
Angela

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