Hello amber users,
I tried to extract energy of protein from protein-sugar interaction MD
trajectory using imin=5.
As Carlos said, I used "-x" option to read the previous trajectory and
calculate energy for protein only.
What I did are:
1. MD simulation of protein-sugar in the gas phase
2. strip sugar from trajectory and save to new trajectory
(MDtraj_protein.x) using ptraj
3. create topology (protein.top) and coordinates (protein.crd) files
for protein only in xleap
4. load new trajectory using imin=5 and calculate energy
Here are input and command to run calculation:
&cntrl
imin = 5, ntx = 1, maxcyc=1,
scnb = 2.0, scee = 1.2,
cut = 9999.0
/
sander -O -i proteinE.in -o proteinE.out -p protein.top -c protein.crd
-x MDtraj_protein.x
However, I don't get any output file.
There is nothing in proteinE.out file.
What is wrong with my input or command?
Is there anyone to have same problem and can you help me?
Thanks
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Received on Wed Jul 11 2007 - 06:07:52 PDT
