AMBER Archive (2008)

Subject: Re: AMBER: ff99 (PK/IDIVF)

From: saurabh agrawal (imsam100_at_yahoo.co.in)
Date: Tue Dec 16 2008 - 05:47:09 CST

Dear Sir,

Thank you for your guidance.

I was trying to filter torsional angle parameters for some amino acids and dyes. I tried to save lib file using saveoff command at xleap but unable to get torsion angle parameters in the file. While looking at parm99.dat I found that it has different Pk values for different phase angle and last term (??) as for example given below.

CT-CT-N-C    1    0.50        180.0           -4.         phi,psi,parm94
CT-CT-N-C    1    0.15        180.0           -3.         phi,psi,parm94
CT-CT-N-C    1    0.00          0.0            -2.         JCC,7,(1986),230
CT-CT-N-C    1    0.53          0.0             1.         phi,psi,parm94

Now may you tell me which one could be appropriate for general perpose? Or how can I get torsion angle parameters for a particular molecule?

Thanking you in advance.

Sincere Regards,

Saurabh

--- On Mon, 15/12/08, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:
From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
Subject: Re: AMBER: ff99 (PK/IDIVF)
To: amber_at_scripps.edu
Date: Monday, 15 December, 2008, 12:08 AM

Po is phase, but Pk is NOT omega. it is V. the torsion angle is measured from the coordinates.

On Sun, Dec 14, 2008 at 1:29 PM, saurabh agrawal <imsam100_at_yahoo.co.in> wrote:

Dear Dr. Simmerling and Dr. Walker,

Thank you for your valuable comments and  help.

I am just willing to clarify one more query:  Is Po stands for phase angle (gamma) and Pk/IDIVF is torsion angle (omega)?

Thanking you in advance.

Sincere regards,

Saurabh

--- On Fri, 12/12/08, Ross Walker <ross_at_rosswalker.co.uk> wrote:

From: Ross Walker <ross_at_rosswalker.co.uk>
Subject: RE: AMBER: ff99 (PK/IDIVF)

To: amber_at_scripps.edu
Date: Friday, 12 December, 2008, 10:36 PM

 
 

Hi Saurabh

  

To follow up on Carlos's excellent explanation I would just like
to add that this of course only applies to the use of wildcards (X-) in dihedral
terms. This is something that has always concerned me in AMBER because it makes
it very difficult to understand what is going on. Additionally the assumption
(made by the idivf value) is in my opinion dangerous since one could almost
certainly find molecules (not necessarily in the amino acid set but elsewhere)
that had different connectivity for that wild card dihedral.

  

My advice if you are generating your own parameters is to ALWAYS
explicitly define all dihedrals and in all cases set idivf=1 and set the
barrier height appropriately for that specific dihedral. This will avoid much
confusion and chances for mistakes.

  

All the best

Ross

  

From:
owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of Carlos
Simmerling

Sent: Friday, December 12, 2008 6:05 AM

To: amber_at_scripps.edu

Subject: Re: AMBER: ff99 (PK/IDIVF)

  

the k value used in the
dihedral function is pk, but this is the total for rotating that bond (in this
case 14.5). since there are multiple sets of 4 atoms that contribute, the total
is divided by the idivf, the expected number of 4-atom-sets that will have this
applied. each will get in this case 1/4 of the total (1 over the first number
after the x-c-c-x in the .dat file), or 3.625.

the 2 in red is the periodicity of this dihedral term - see http://ambermd.org/eqn.txt

 

On Fri, Dec 12, 2008 at 8:26 AM, saurabh agrawal <imsam100_at_yahoo.co.in> wrote:

 
  
  Dear Amber
  Users,

  

  

  In xleap leaprc.ff99 parameters looks like:

                  
  N     Pk/IDIVF   
  Po

  ?-c-c-?       2    
  3.6250        Pi

  

  While In parm99.dat file torsional angle parameters are as given:

  

  x-c-c-x     
  4       
  14.50      
  180         2

  

  May some one explain the meaning of Pk/IDIVF (red) field in torsional angle
  parameters in the ff99 force field and and the formula to calculate it.

  Also the caption of the fields in the parm99.dat file.

  

  Sincere regards,

  

  Thanking you in advance.

  

  Saurabh
  
 

  

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