Re: [AMBER] Soft-core questions for TI method

From: Ying-Chieh Sun <>
Date: Wed, 30 Oct 2013 16:31:57 +0800

I recalled the tolerance of difference in coordinates of common atoms is
0.001 A. A good practice is to generate child coordinate file by copying
parent file, and then modify the copied file. Hope this help. Ying-chieh

-----Original Message-----
From: yuandandan []
Sent: Monday, October 7, 2013 3:43 PM
Subject: [AMBER] Soft-core questions for TI method


I encountered a question when I used soft-core for Thermodynamic Integration
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
     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 didn't keep the same in 0
and 1 when compare the two output .rst files, and then the equilibrium
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!
Dandan yuan, PHD students
Nanjing University

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Received on Wed Oct 30 2013 - 02:00:08 PDT
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