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
