[AMBER] error on open distatance restraint

From: gmail <heptoking.gmail.com>
Date: Sat, 24 Jan 2009 10:58:27 +0800

Dear All
    After trying a dozen times on fixing the problem on distance restraint file, I still have not come up with a solution.

I am trying to simulate a big protein (over 500 residues) and a inhibitor solvated in water.
    Next I tried to make a distance restraint file using makeDIST_RST command. However, this program limit the system to
less then 5000 atoms. Okay, I tried to make a RST file on my own. Here is the RST file:

#
# 476 THR N 564 JPC O22 2.684
&rst iat= 7408, 8818, r1= 1.30, r2= 1.80, r3= 2.684, r4= 3.1, rk2=0, rk3=20.0, ir6=1, ialtd=0,/
#
#
# 477 TYR N 564 JPC O21 2.717
&rst iat= 7422, 8817, r1= 1.30, r2= 1.80, r3= 2.717, r4= 3.2,/
#
#
# 422 ARG CB 564 JPC 3Cl1 3.512
&rst iat= 6552, 8839, r1= 1.30, r2= 1.80, r3= 3.512, r4= 4.0, /


and run the heating step, the input are as follows:



Heating up from 0 K to 300 K
       
&cntrl
  imin=0,irest=0,ntx=1,
  nmropt=1,
  nstlim=25000,dt=0.002,
  ntc=2,ntf=2,
  cut=12.0, ntb=1,
  ntpr=500, ntwx=500,
  ntt=3, gamma_ln=2.0,
  tempi=0.0, temp0=300.0,
/
 &wt type='REST', istep1=0,istep2=3000,value1=0.1,
            value2=1.0, /
 &wt type='REST', istep1=3001,istep2=25000,value1=1.0,
            value2=1.0, /
&wt type='END'/
LISTOUT=POUT
DISANG=RST


But sander keep telling me: unit 33 error on opening RST file. I checked carefully that the RST filename is correct.
and I even check the fileformat is Unix not DOS using vi command.

The detailed output is here,

          -------------------------------------------------------
          Amber 9 SANDER 2006
          -------------------------------------------------------

| Run on 01/24/2009 at 10:25:59
  [-O]verwriting output

File Assignments:
| MDIN: heat_rest.in
| MDOUT: heat.out
|INPCRD: min.rst
| PARM: forcedock.prmtop
|RESTRT: heat.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: heat.mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip


 Here is the input file:
 
                                        
Heating up from 0 K to 300 K
                                                                               
&cntrl
  imin=0,irest=0,ntx=1,
  nmropt=1,
  nstlim=25000,dt=0.002,
  ntc=2,ntf=2,
  cut=12.0, ntb=1,
  ntpr=500, ntwx=500,
  ntt=3, gamma_ln=2.0,
  tempi=0.0, temp0=300.0,
/
 &wt type='REST', istep1=0,istep2=3000,value1=0.1,
            value2=1.0, /
 &wt type='REST', istep1=3001,istep2=25000,value1=1.0,
            value2=1.0, /
&wt type='END'/
LISTOUT=POUT
DISANG=RST

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

| Flags:
 getting new box info from bottom of inpcrd
| INFO: Old style inpcrd file read

| peek_ewald_inpcrd: Box info found
|Largest sphere to fit in unit cell has radius = 39.087

  Unit 33 Error on OPEN: RST


I checked the tutorial on NMR and compared the RST file for error but with no solution.

And I checked the mailing list archive but seems no similar question was posted.



So please give me some suggestions on this.



Cheers...



Xiaonan Zhang

Shanghai public health clinical center






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Received on Sun Jan 25 2009 - 01:15:51 PST
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