[AMBER] error in distance restraint input file

From: Michael Shokhen <michael.shokhen.biu.ac.il>
Date: Fri, 26 Oct 2018 10:31:12 +0000

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>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Oct 26 2018 - 04:00:03 PDT
Custom Search