AMBER Archive (2008)

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

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Tue Dec 16 2008 - 06:01:32 CST

these are protein phi/psi parameters and should not be used for general
purpose.

getting torsion angles is far too complex for simply reading an email. there
are many papers published where people explain their procedure. there are
also Amber tutorials for this. I suggest that you look at peer-reviewed
journal articles that have successfully done what you are trying to
accomplish, and follow the procedure that they have used.
in my opinion, generating force fields is an advanced topic and really
should be done by someone that already has lots of experience in using
existing force fields. you might also consider the automated tools for doing
this, such as antechamber and gaff. carefully read the articles related to
those first (how they were developed, and also articles in which these are
used so you have an idea of what kind of problems can be solved using them).
there is simply no substitute for extensive reading of the literature prior
to undertaking a project.

good luck!

On Tue, Dec 16, 2008 at 6:47 AM, saurabh agrawal <imsam100_at_yahoo.co.in>wrote:

> 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<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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