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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Received on Fri Jul 18 2003 - 23:53:00 PDT
