Dear All,
I have followed a tutorial about MD simulation on DNA in Mixed Water-Ethanol Solvent (
http://ludwig.chem.wesleyan.edu/~sergei/tutorial-2.htm).
The first two steps (min and init) had worked out. But the third, where I am supposed to run shake has not worked:
After typing: $AMBERHOME/exe/sander -O -i Etohshake.in -p ETOHBOX.top -c ETOHBOX_init.rst -oETOHBOX_shake.rst -x ETOHBOX_shake.crd
forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read
Image PC Routine Line Source
sander 081A8716 Unknown Unknown Unknown
sander 081A6DE9 Unknown Unknown Unknown
sander 0817AB45 Unknown Unknown Unknown
sander 081453D2 Unknown Unknown Unknown
sander 08145102 Unknown Unknown Unknown
sander 081538A9 Unknown Unknown Unknown
sander 080D6669 Unknown Unknown Unknown
sander 080D637D Unknown Unknown Unknown
sander 080A9075 Unknown Unknown Unknown
sander 08073F90 Unknown Unknown Unknown
sander 08073CA2 Unknown Unknown Unknown
sander 08049901 Unknown Unknown Unknown
libc.so.6 AFDCC974 Unknown Unknown Unknown
sander 08049821 Unknown Unknown Unknown
Inside the ETOHBOX_shake.rst there is the followed message:
-------------------------------------------------------
Amber 8 SANDER Scripps/UCSF 2004
-------------------------------------------------------
| Run on 04/03/2007 at 10:12:08
[-O]verwriting output
File Assignments:
| MDIN: Etohshake.in
| MDOUT: ETOHBOX_shake.rst
|INPCRD: ETOHBOX_init.rst
| PARM: ETOHBOX.top
|RESTRT: restrt
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: ETOHBOX_shake.crd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
Here is the input file:
md of ethanolbox
&cntrl
imin=0,
ntx=7,irest=1,ntrx=1,
ntxo=1,ntpr=25,ntwr=500,iwrap=0,
ntwx=500,ntwe=25,
ntf=2,ntb=2,dielc=1.0,igb=0,
scnb=2.0,scee=1.2,
ipol=0,
ibelly=0,ntr=0,
nstlim=10000,
t=0.0,dt=0.002,
temp0=300,tempi=100.0,
ig=71277,
ntt=1,tautp=1.0,
vlimit=0.0,
ntp=1,pres0=1.0,comp=44.6,taup=1.0,
ntc=2,tol=0.00005,
&end
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags:
getting new box info from bottom of inpcrd
~
~
I kindly ask if someone can help me to find out why there is a problem, if I'm doing exactly what the tutorial says.
If someone has some ideas or other input files to do minimization, equilibration of an ethanol box, (first NVT from 100K until 300K, then NPT at 300K, in order to equilibrate the density), it would help me a lot, since it is the first time I'm using sander.
Thanks in advance.
Rita Leite
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Received on Wed Apr 04 2007 - 06:07:37 PDT
