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
