Dear D Case,
I again run some experiments according to your advices and my min.out file is like in below. I used packmol, I wrote box size for x, y, z : 9.825 A and created a packmol pdb file for this system. So I didn't use solvatebox command in xleap. I thought that there is a problem about using packmol. If so, How can I solve this problem and use packmol without any errors ? In this sense, I'm waiting for your help and also other people's help who have enough experience on PACKMOL package. Or I'm waiting for some alternative solutions of you related with LEAP.
Sincerely,
-------------------------------------------------------
Amber 10 SANDER 2008
-------------------------------------------------------
| PMEMD implementation of SANDER, Release 10
| Run on 01/26/2009 at 15:55:22
[-O]verwriting output
File Assignments:
| MDIN: /home_palamut2/ogurbulak/c7AMBER10/min/min.in
| MDOUT: /home_palamut2/ogurbulak/c7AMBER10/min/min.out
| INPCRD: /home_palamut2/ogurbulak/c7AMBER10/n-dodecane.inpcrd
| PARM: /home_palamut2/ogurbulak/c7AMBER10/n-dodecane.prmtop
| RESTRT: /home_palamut2/ogurbulak/c7AMBER10/min/n-dodecane.rst
| REFC: refc
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
| MDINFO: mdinfo
|LOGFILE: logfile
Here is the input file:
initial minimization
&cntrl
imin=1,
maxcyc=500,
ncyc=250,
ntb=1,
cut=9.825,
ntpr=100,
ntc=2, ntf=2,
/
| ERROR: Box parameters not found in inpcrd file!
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Received on Wed Jan 28 2009 - 01:13:51 PST
