Dear AMBER users:
I am trying to get the deltaH using nmode module in AMBER package for complex,
protein and ligand, after several
try, at first it said the memory is not enough. After I increased the sizes.h
file and ran it again, it can go through the minimization step. However, when
calculating the nmode step, it always gives me error message. At first the drms
in both nmode_min.in and nmode.in is 0.00001. Then it tells me that the RMS
gradient from input (after minimization) is bigger than the required 0.00001.
Then I increase the drms in nmode.in to 0.00005. However, it gave me the core
dump file. Another point I want to point out is that no matter I ran it in the
formatted or unformatted form, it gave me the same result. THat means, the
minimization step was always ok, but the nmode step was always not ok. The
related .in file is attached as follows. By the way, the system is around 88
amino acids to 99 amino acids.
Can someone give me a hand? Thank you very much.
Haizhen Zhong
File in nmode_min.in
minimization, saving coords in binary
&data
ntrun=4,
nsave=2,
ndiag=2,
cut=95.0,
nprint=100,
drms=0.00001,
maxcyc=100,
bdwnhl=0.01,
dfpred=0.1,
scnb=2.0,
scee=2.0,
nvect=200,
ntxo=1
&end
File of nmode.in
&data
ntrun = 1, nsave=2, ndiag=2, cut=95.0, ibelly=0, ntx=1,
nprint=1, ioseen=0,
drms = 0.00005, maxcyc=1, bdwnhl=1.1, dfpred = 0.1,
scnb=2.0, scee=2.0, idiel=0,
nvect=200
&end
log file
Amber demo/crown_ether: normal mode analysis
nmode: minimization of crown in vacuum:
nmode: frequencies and thermodynamic analysis:
Segmentation fault (core dumped)
Received on Thu Aug 08 2002 - 06:56:08 PDT
