Dear AMBER Experts,
AMBER16 that I have on my server reports error message
for the file rst.dist that I have generated to define harmonic restraints on
several interatomic distances formed by Ca(2+) cation with small molecule ligand (MOL)
chelating it.
I need your help in the correct generation of the rst.dist file
that I hope will resolve the problem.
See details below.
Thank you,
Michael
I have ran the job by the command:
setenv CUDA_VISIBLE_DEVICES '0,1'
nohup mpirun -np 2 $AMBERHOME/bin/pmemd.cuda.MPI -O -i eq.in -o eq.out -p ../mc.prmtop -c ../5_/density.rst -r eq.rst -ref ../5_/*.rst &
The input eq.in file is:
equilibrate 10ns
&cntrl
imin=0,irest=1,ntx=5,
nstlim=5000000,dt=0.002,
ntc=2,ntf=2,ig=-1,
cut=10.0, ntb=2, ntp=1, taup=2.0,
ntpr=1000, ntwx=1000,
ntt=3, gamma_ln=2.0,
temp0=310.0,
ntr=1,nmropt = 1,
&end
&wt
type='END',
&end
DISANG=rst.dist
The distance restraints rst.dist file is:
#
# 349 CA CA 1 MOL O1 2.5
&rst
iat= 5752, 5832, r1= 1.80, r2= 2.30, r3= 2.50, r4= 3.0,
rk2=50.0, rk3=50.0,
&end
#
# 349 CA CA 1 MOL O4 2.5
&rst
iat= 5752, 5839, r1= 1.80, r2= 2.30, r3= 2.50, r4= 3.0, &end
#
# 349 CA CA 1 MOL O5 2.7
&rst
iat= 5752, 5840, r1= 2.00, r2= 2.50, r3= 2.70, r4= 3.2, &end
#
# 349 CA CA 1 MOL O6 2.7
&rst
iat= 5752, 5847, r1= 2.00, r2= 2.50, r3= 2.70, r4= 3.2, &end
#
# 349 CA CA 1 MOL O8 2.5
&rst
iat= 5752, 5864, r1= 1.80, r2= 2.30, r3= 2.50, r4= 3.0, &end
#
# 349 CA CA 1 MOL O9 2.5
&rst
The error message in the output eq.out file is:
LOADING THE CONSTRAINED ATOMS AS GROUPS
5. REFERENCE ATOM COORDINATES
default_name
----- READING GROUP 1; TITLE:
DISANG=rst.dist
GROUP 1 HAS HARMONIC CONSTRAINTS 0.00000
rfree: End of file on unit 5
*****************************
Michael Shokhen, PhD
Associate Professor
Department of Chemistry
Bar Ilan University,
Ramat Gan, 52900
Israel
email: shokhen.mail.biu.ac.il<https://webmail.biu.ac.il/owa/redir.aspx?C=a160ef9b9a6b4d06992402715d3ee465&URL=mailto%3ashokhen%40mail.biu.ac.il>
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Received on Fri Oct 26 2018 - 04:00:03 PDT
