Dear users
I ran a min. step for 2500 steps.
Since the energy was not stable and the RMS still high i decided to run a second min. (2500 additional steps) using as starting point the files i got from the previous step.
In the first step:
-r PknGAde-min.rst and -ref PknGAde-solv-min.rst
The 2nd step input file was the following:
Initial XMIN minimisation of PknG-Adenine complex: complex, water and ions
&cntrl
imin=1,
maxcyc=2500,
ntmin=3,
irest=1,
ntx=5,
ntb=1,
igb=0,
ntr=0,
cut=10,
ntpr=10, ntwx=10, ntwr=1000
And i ran sander as follow:
sander -O -i PknGAde-min.in -o PknGAde-min.out -p ../PknGAde_params/PknGHAdeH_ion_wt.prmtop -c PknGAde-min.rst -r PknGAde-min.rst -ref PknGAde-solv-min.rst -x PknGAde-min.mdcrd &
Thus I used as coord. the file I got from the previuos min.
I got the following error:
ERROR: I could not find enough velocities in
PknGAde-min.rst
I do not understand why i got that error.
Anyone can help me in understanding what happened?
Thank you
Valentina
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Valentina Romano | PhD Student | Biozentrum, University of Basel & SIB Swiss Institute of Bioinformatics
Klingelbergstrasse 61 | CH-4056 Basel |
Phone: +41 61 267 15 80
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Received on Tue May 20 2014 - 09:30:03 PDT
