AMBER Archive (2006)

Subject: AMBER: Problem with sander in Linux

From: Wimal (wimal_at_boc.uu.se)
Date: Mon Aug 14 2006 - 03:14:00 CDT

Dear Sir/ Madam,

We are using Amber 7 on Red Hat Linux system. While we are performing
a NMR-restrained moleculacular dynamics simulation step using sander,
we could not run a script which include a heating step from 100K to
298K. There I find an error message in the output file:

| Flags:
 getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
 Warning: Error opening "Old" file from subroutine OPNMRG
 File = ./Md_RST

Could you please kindly let me know what the problem with our simulation is?
I am sending the input and output files used in sander as attachments.

Thanking you,
 
Yours Sincerely,

Wimal Pathmasiri. 

-- 
Ph.D. Student
Department of Bioorganic Chemistry
Uppsala University
BMC, Box 581
SE-75123 Uppsala
Sweden.

Phone: 0046184714980
Fax:   004618554495

          -------------------------------------------------------
          Amber 7 SANDER Scripps/UCSF 2002
          -------------------------------------------------------

| Sat Aug 5 00:02:40 2006

  [-O]verwriting output

File Assignments:
| MDIN: Int_Md_Heat.in
| MDOUT: Int_Md_Heat.out
|INPCRD: SA_60.2.rst
| PARM: RA_cio_wat.prmtop
|RESTRT: Int_Md_Heat.rst
| REFC: SA_60.2.rst
| MDVEL: mdvel
| MDEN: Int_Md_Heat.nrj
| MDCRD: Int_Md_Heat.mdcrd
|MDINFO: Int_Md_Heat.mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

 Here is the input file:

Initial dynamics w/ belly on RNA, 8.0 cut, SHAKE
                              
 &cntrl
                                                                       

                                                                              
  nmropt = 1, ipnlty = 1,
                                               
  ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
            
  ntpr = 100, ntwx = 500, ntwv = 0, ntwe = 0,
            

                                                                              
  ntc = 2, tol = 0.00001,
                                         
  ntf = 2, ntb = 2, dielc = 1.0,
                           
  cut = 8.0,
                                                          
  scnb = 2.0, scee = 1.2,
                                           

                                                                              
  ibelly = 0, ntr = 0, imin = 0,
                             
       
                                                                       
  nstlim = 20000,
                                                             
  t = 0.0, dt = 0.0015,
                                          

                                                                              
  temp0 = 300.0, tempi = 100.0,
                                        
  ig = 71277, heat = 0.0,
                                             
  ntt = 1,
                                                           
  tautp = 0.2,
                                                               
  vlimit = 15.0,
                                                              

                                                                              
  ntp = 1, pres0 = 1.0, comp = 44.6,
                          
  taup = 0.2, npscal = 1,
                                               

                                                                              
  jfastw = 0,
                                                          
 &end
                                                                         
 &ewald
                                                                       
  a=34.9927920 b=37.1218096 c=40.8344006
      
 &end
                                                                         
 &wt
                                                                         
   type='TEMP0', istep1=0, istep2=2000,
                                   
                 value1=100.0, value2=298.0,
                                 
 &end
                                                                         
 &wt
                                                                         
   type='TEMP0', istep1=2001, istep2=20000,
                                 
                 value1=298.0, value2=298.0,
                                  
 &end
                                                                         
 &wt
                                                                         
   type='REST', istep1=0, istep2=2000, value1=0.0, value2=1.0,
             
 &end
                                                                         
 &wt
                                                                         
   type='REST', istep1=2001, istep2=30000, value1=1.0, value2=1.0,
         
 &end
                                                                         
 &wt type='END', &end
                                                         
DISANG=./Md_RST
                                                           
LISTOUT=POUT
                                                                  

--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags:
 getting new box info from bottom of inpcrd
| peek_ewald_inpcrd: Box info found
 Warning: Error opening "Old" file from subroutine OPNMRG
 File = ./Md_RST

Initial dynamics w/ belly on RNA, 8.0 cut, SHAKE
 &cntrl

  nmropt = 1, ipnlty = 1,
  ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
  ntpr = 100, ntwx = 500, ntwv = 0, ntwe = 0,

  ntc = 2, tol = 0.00001,
  ntf = 2, ntb = 2, dielc = 1.0,
  cut = 8.0,
  scnb = 2.0, scee = 1.2,

  ibelly = 0, ntr = 0, imin = 0,
       
  nstlim = 20000,
  t = 0.0, dt = 0.0015,

  temp0 = 300.0, tempi = 100.0,
  ig = 71277, heat = 0.0,
  ntt = 1,
  tautp = 0.2,
  vlimit = 15.0,

  ntp = 1, pres0 = 1.0, comp = 44.6,
  taup = 0.2, npscal = 1,

  jfastw = 0,
 &end
 &ewald
  a=34.9927920 b=37.1218096 c=40.8344006
 &end
 &wt
   type='TEMP0', istep1=0, istep2=2000,
                 value1=100.0, value2=298.0,
 &end
 &wt
   type='TEMP0', istep1=2001, istep2=20000,
                 value1=298.0, value2=298.0,
 &end
 &wt
   type='REST', istep1=0, istep2=2000, value1=0.0, value2=1.0,
 &end
 &wt
   type='REST', istep1=2001, istep2=30000, value1=1.0, value2=1.0,
 &end
 &wt type='END', &end
DISANG=./Md_RST
LISTOUT=POUT

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu