QUESTION ABOUT SANDER

From: Ramon Garduno <ramon_at_ce.fis.unam.mx>
Date: Fri 08 Dec 2000 21:13:31 PST

Dear Amber users:

I have what it seems a FAQ but I can not get out of it. I am using AMBER 5.1

I have been running an equilibration process for a beta-cyclodextrin inclusion
complex with an small molecule (ldopa) with explicit waters. 172 atoms in
solute and 4^3 water cubes.

I am following the amber tutorial on polyA-polyT equilibration. Thus, I am
using the same parameter values for input files at: 1) minimization holding
the solute fixed, 2) Dynamics holding the solute fixed, and 3) Dynamics
holding the solute fixed, but using PME method.

Everything goes well up to the third equilibration step. The cell dimensions
are 31.6869611 32.1965768 26.9307941 for 4^3 water cubes.

I have tested the following changes....
A) Use of previously optimized solute before adding water.
B) Use of 3^3 and 4^3 water cubes....5^3 water cubes gives me an error on
   water molecules over the limit.
C) Use NTT=1 and NTT=5 with TAUTP=TAUTS=0.2, VLIMIT=20.
However I keep on obtaining the same message every time I try different
parameters. The message is...

 vlimit exceeded for step 4167; vmax = 20.82020614631265
 vlimit exceeded for step 4176; vmax = 21.27704551382417
 vlimit exceeded for step 4180; vmax = 21.65670561814358
 vlimit exceeded for step 4189; vmax = 21.55409480978921

 COORDINATE RESETTING CANNOT BE ACCOMPLISHED,
 DEVIATION IS TOO LARGE
 NITER, NIT, LL, I AND J ARE : 0 4 73 153 154

It is necessary to mention that the very same numbers appear time after time.
So I imagine that the problem is located at atoms 153 and 154 (fixed solute
atoms). This is an O-H bond, but I am using NTF=2 , NTP=1 and NTC=2.

I have tried all the hints mentioned at amber tutorial on BLOW UPs but
it does not help me at all.

Any suggestion will be appreciated.

Much obliged,

Ramon 

--
		"There are so many ways....
			There is so little time...."
		"Hay tantos caminos.....
			Pero, hay tan poco tiempo....."
___________________________________________________________________________
		  	 Dr. Ramon Garduno-Juarez
                     Research Professor in Biophysics
CENTRO DE CIENCIAS FISICAS          | EMAIL:  ramon_at_ce.fis.unam.mx
UNIVERSIDAD NAL. AUTONOMA DE MEXICO |
Apdo. Postal 48-3                   | VOICE:  +52(5)6227749 ; +52(7)3291749
62251 Cuernavaca, Morelos           | 
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___________________________________EOF ____________________________________
From Ryan.H.Lilien_at_Dartmouth.EDU 11 Dec 2000 11:35:35 EST
Message-id: <38071530.dasher.Dartmouth.EDU>
Date: 11 Dec 2000 11:35:35 EST
From: Ryan H. Lilien <Ryan.H.Lilien_at_Dartmouth.EDU>
To: AMBER list <amber.heimdal.compchem.ucsf.edu>
Subject: ANAL question
In-Reply-to: <00120618193500.10500.pi3-pc68>
Hello,
  I'd like to use the ANAL program to determine the energy of a fixed system.  Starting with a PDB file I ran that file through xleap and generated the .top and .crd files and feel that I'm almost ready to run anal, however I don't know how to setup an anal input control data file.  I have read the manual pages for anal but I don't understand how to ste the control variables in the input control data file.  I looked around the amber distribution but couldn't find an example input file.  Would it be possible to either point me toward additional documentation or send me an example anal input control data file?
I am currently working in Amy Anderson and Rob O'Neil's lab and they have a licenced copy of Amber 6.0.
Thank you,
Ryan Lilien
Department of Computer Science
Dartmouth College
Hanover, NH  03755
From Ryan.H.Lilien_at_Dartmouth.EDU 11 Dec 2000 13:29:07 EST
Message-id: <38075329.dasher.Dartmouth.EDU>
Date: 11 Dec 2000 13:29:07 EST
From: Ryan H. Lilien <Ryan.H.Lilien_at_Dartmouth.EDU>
To: AMBER list <amber.heimdal.compchem.ucsf.edu>
Subject: ANAL question
In-Reply-to: <00120618193500.10500.pi3-pc68>
This morning I sent the attached email, however I was able to find some example files and believe I now understand how to use anal.
Thank you,
Ryan Lilien
>Date: 11 Dec 2000 11:35:35 EST
>From: Ryan H. Lilien
>Subject: ANAL question
>To: amber_at_cgl.ucsf.edu
Hello,
  I'd like to use the ANAL program to determine the energy of a fixed system.  Starting with a PDB file I ran that file through xleap and generated the .top and .crd files and feel that I'm almost ready to run anal, however I don't know how to setup an anal input control data file.  I have read the manual pages for anal but I don't understand how to ste the control variables in the input control data file.  I looked around the amber distribution but couldn't find an example input file.  Would it be possible to either point me toward additional documentation or send me an example anal input control data file?
I am currently working in Amy Anderson and Rob O'Neil's lab and they have a licenced copy of Amber 6.0.
Thank you,
Ryan Lilien
Department of Computer Science
Dartmouth College
Hanover, NH  03755
Received on Fri Dec 08 2000 - 21:13:31 PST
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