I am running a simple minimization of RB69, Pol-alpha, using sander_classic. Below is my input file. I am using .prmtop and .inpcrd files before any water or ions have been added. I am having a problem with my output file numbers. After the first run, I get "nan" values for everything. Do you think it is a problem with my structure or with my input file?
Input:
Relaxation of Hydrogen holding all heavy atoms still
&cntrl
ntpr=1,
ntf=1, idiel=0, dielc=1, scnb=2, scee=1.2, cut=10.0
imin=1, maxcyc=100, ncyc=100, ntmin=1, ntwe=10, ntwxm=0,
ntr=1, ntwx=1, ntwem=0,
&end
Group input for restraining the Protein and DNA heavy atoms
5000
FIND
* * M *
SEARCH
RES 1 934
END
END
Output after one step:
NSTEP ENERGY RMS GMAX NAME NUMBER
1 nan nan 3.9408E+08 O 16661
BOND = 903.6790 ANGLE = 2606.6465 DIHED = 8287.9576
VDWAALS = 23532619.7971 EEL = -24232.1835 HBOND = 0.0000
1-4 VDW = nan 1-4 EEL = inf CONSTRAINT = 0.0000
Thank you,
Angela Pantelogianis
Received on Mon Jul 14 2003 - 17:53:00 PDT
