Dear Amber user:
I am trying to simulate modified PNA- DNA .
PNA ( in which the whole phosphodiester backbone of DNA is replaced with 2-Aminoethylglycine backbone.)
Modified PNA (adenine base is also modified ).
I have stuck with an error
Id.so.1: sander: fatal: libsunperf .so. 2: open failed No such file or directory
/opt/age/default/spool/tentacle6/job_scripts/1101: line 5: 10035 killed
$AMBERHOME/exe/sander –o -i wat_nsd_md3.in -o wat_nsd_md3.out -p wat_nsd.prmtop -c wat_nsd_md2.rst -r wat_nsd_md3.rst -ref wat_nsd_md2.rst -x wat_nsd_md3.mdcrd
gzip: wat_nsd_md3.mdcrd: no such file or directory
My input file wat_nsd_md3.in is
nsd 15-mer: 10ps MD with res(10.0) on nsd
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 10,
ntr = 1,
ntc = 2,
ntf = 2,
tempi = 0,
temp0 = 300.0,
ntt = 3,
gamma_ln = 1,
nstlim = 5000, dt = 0.002,
ntpr = 250, ntwx = 250, ntwr = 10000
/
Hold the nsd fixed
10.0
RES 1 16
END
END
Charges on PNA backbone taken from reference JACS, 1998, 120, 5895-5904
But the charge on modified base is calculated from gaussian (03W).
I have got reliable results in case of normal PNA-DNA simulation with the same input files.
any body help me why this is happened in case of modified PNA.
Thanks
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Received on Sun Oct 14 2007 - 06:07:05 PDT
