AMBER Archive (2008)

Subject: AMBER: for NMR refinement

From: Wenyong Tong (wenyong_tong_at_yahoo.com)
Date: Thu Feb 28 2008 - 20:20:08 CST

Hello Dr. Case,
 
Basically, these two annealing protocol are the same as posted here before except the following weight changes that I mistakenly typed.
 
 TAUTP 0 50000 0.200000 0.200000 0 0
 TAUTP 50001 20000 4.000000 2.000000 0 0
 Warning: ISTEP1 >= ISTEP2
 TAUTP 20001 88000 1.000000 1.000000 0 0
 TAUTP 88001 100000 0.500000 0.500000 0 0
 TAUTP 100001 200000 0.010000 0.050000 0 0
 REST 0 500000 0.100000 1.000000 0 0
 REST 500001 200000 1.000000 1.000000 0 0
 Warning: ISTEP1 >= ISTEP2
 
Although I got warnings, the annealing still works and result is even better than correct one from the aspects of ETOT(-50 vs. 25) and total distance penalty( 70 vs. 120).
 
I was wondering how AMBER recognizes these weight changes with warnings and works and how I should correct it.
 
Thanks in advances
 
Wenyong

 

----- Original Message ----
From: David A. Case <case_at_scripps.edu>
To: amber_at_scripps.edu
Sent: Thursday, February 28, 2008 6:47:10 PM
Subject: Re: AMBER: problems with 10-12 potential in amber8 sander

On Thu, Feb 28, 2008, Amie Demmel wrote:

> It seems that we increased the limit in both amber8(at line 81 in rdparm.f the
> check is to 2000) and sander5.0.1 (that check is to 6000). Since our group
> deals with coarse grain models that requires each residue on the protein to be
> considered "unique". Is there a way to safely increase nphb?

Did you also change the sizes of the asol and bsol and hbcut arrays in
parms.h? Note that you also have to change BC_PARMR and BC_PARMI in parms.h
(see the comments) if you are planning to run in parallel.

[It is clear that better code would make all of this stuff dynamic, so
that array bounds were determined at run time. Until then, however, you will
have to take care to make sure you have enough space in these arrays.]

...dac
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