AMBER: running MD simulatons

From: sachin patil <sachin_ppatil.yahoo.com>
Date: Tue, 6 Jul 2004 09:52:58 -0700 (PDT)

Hi,
I am trying to MD simulations on a system consisting
of
effects of water molecules on a peptide bound to a
protein. Here is my input file. (I have prepared the
input file which is consistent with the input file
mentioned in the HIV-integrase tutorial.)
I have run couple of stages of minimizations and I am
running the MD simulations in the third step.
---------------------------------------------------------

 Heating up the system equilibration stage 1
 &cntrl
  nstlim=5000, dt=0.002, ntx=1, irest=0, ntpr=500,
ntwr=5000, ntwx=5000,

  tempi =100.0, temp0=300.0, ntt=1, tautp=2.0,
ig=209858,
 
  ntb=1, ntp=0,

  ntc=2, ntf=2,
 
  nrespa=2,
&end
--------------------------------------------------------
when I feed this to sander with command-

% sander -O -i step3_eq_v.in -p MDrun.parm7 -c
  2stepoutput_min_all.rst -r 3stepoutput_eq_v.rst -x
  3stepoutput_eq_v.crd -o 3stepoutput.out

It hangs up creating an empty 3stepoutput.out.
 Interestingly, if I substitute temp0 as above to
tempo
that is I replaced 0 (zero) with o (alphabet o) it
gives me 3stepoutput.out file which looks like and
then
an error message-




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

| Tue Jul 6 12:51:31 2004

  [-O]verwriting output

File Assignments:
| MDIN: step3_eq_v.in
                         
| MDOUT: 3stepaoutput.out
                    
|INPCRD: 2stepoutput_min_all.rst
                        
| PARM: MDrun.parm7
                    
|RESTRT: 3stepoutput_eq_v.rst
                        
| REFC: refc
                        
| MDVEL: mdvel
                        
| MDEN: mden
                        
| MDCRD: 3step_eq_v.crd
                    
|MDINFO: mdinfo
                        
|INPDIP: inpdip
                        
|RSTDIP: rstdip
                        


 Here is the input file:

 # Heating up the system equilibration stage 1
 &cntrl
  nstlim=5000, dt=0.002, ntx=1, irest=0, ntpr=500,
ntwr=5000, ntwx=5000,
 tempi=100.0, temp0=300.0, ntt=1, tautp=2.0,
ig=209858,

  ntb=1, ntp=0,

  ntc=2, ntf=2,

  nrespa=2,
  &end
END
END
--------------------------------------------------------
namelist read: variable not in namelist
apparent state: unit 5 named 1HHI_eq_v.in
last format: list io
lately reading sequential formatted external IO
Aborted


Any help and suggestions would be highly appreciated.
                                                      
                 
                      
Sachin Patil
=============
Dept. of Medicinal & Biological Cheistry
University of Toledo
Toledo, Ohio 43606



                
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Received on Tue Jul 06 2004 - 18:53:00 PDT
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