[AMBER] Soft-core questions for TI method

From: yuandandan <yuandandan06.outlook.com>
Date: Mon, 7 Oct 2013 07:43:29 +0000

Hi,




I encountered a question when I used soft-core for Thermodynamic Integration calculation.
 
In fact, I put two molecules into a cage to calculate the relative binding energy
using TI method. Atoms in blue rectangular box (questions.doc in attachment) are the six unique atoms.
 
This is a VDW process.
I created files similar to amber tutorial A9. The files seems all right, the same order and
coordinates for common atoms.
Then, I ran sander. The error is:
 
     Softcore Mask :TWO.C9,H18,H19,C10,O1,O2; matches 6 atoms
     this run corresponds to V0, its softcore atoms interact fully for lambda=0
     this process: 9257 atoms, partner process: 9257 atoms
     Checking for mismatched coordinates.
     WARNING: Local coordinate 1246 differs from partner coordinate 1246 !
     Deviation is small, changing partner coordinate.
     WARNING: Local coordinate 1247 differs from partner coordinate 1247 !
     Deviation is small, changing partner coordinate.
     WARNING: Local coordinate 1248 differs from partner coordinate 1248 !
     Deviation is small, changing partner coordinate.
     WARNING: Local coordinate 1249 differs from partner coordinate 1249 !
 SANDER BOMB in subroutine sc_check_and_adjust
 Atom coordinate disagreement
 Check input files.
 
I checked the files and found that coordinates 1246,12647,1248 correspond to common atom Carbon.
 
Also, I found that the output files of minimization (.out) were finished normal, however,
the coordinates of common atoms didní»t keep the same in 0 and 1 when compare the
two output .rst files, and then the equilibrium failed.
 
The attachment file includes all files for the first window calculation.
Could you please check the file for me and give me any solutions?
Thank you!
 
Best,
 
Dandan yuan, PHD students
Nanjing University
 
 
 
 
 
                                                

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Received on Mon Oct 07 2013 - 01:00:03 PDT
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