AMBER Archive (2008)

Subject: Re: RE: Re: Re: Re: AMBER: AdoMet parameterization with antechamber

From: Jeffrey (jeffry20072008_at_yahoo.cn)
Date: Thu Nov 27 2008 - 09:30:33 CST

Thanks so much for your detailed explanation. It helps me much to get an better understanding of this question. I checked the source code (ephi.f) and found that there were two forms of torsional interaction used in AMBER.

-------
1>. e = pk(ic) * (1.0+phase*cos(pn(ic)*phi)
  where phase = 1.0 or -1.0, and pn = 1,2,3,4, or 6
2>. e = pk*( 1.0+cos(pn*phi-phase) ----- the old energy form,
if phase angle is other than 0 or pi then assume this angle.
------

I tried to determine the PN and PHASE values for each card in AMBER by using the following Vn/2 parameters and corresponding energy values with 1>. or 2>. to solve an equation set, but failed to give the consistent results of the following testing sets(MacroModel output for AdoMet using AMBER FF) :
-----------
         DIHEDRAL ANGLES AND TORSIONAL ENERGIES 137 Proper Torsion interactions present
         --------------------------------------

       Atom Numbers Force Consts Angle Energy
                                  V1/2 V2/2 V3/2 kJ/mol Select Alts Comments FF Line

      1 31 36 37 -0.354 0.521 0.475 17.6 3.656 P3 0 OPT 484
      1 31 36 38 -0.354 0.521 0.475 -99.2 8.874 P3 0 HOPT 484
      1 31 32 33 -0.354 0.521 0.475 173.9 3.102 P3 0 HOPT 484
      1 31 32 34 -0.354 0.521 0.475 -67.1 4.747 P3 0 HOPT 484
      1 31 32 35 -0.354 0.521 0.475 51.6 3.431 P3 0 HOPT 484
-------------

Could you please give me some suggestions on how to determine the PN and PHASE values?

Thanks very much for your time.
Have a nice day. 

---
Jeffrey

 

>Hi Jeffrey,
>
>
>> 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
>
>
>> As stated in JACS1995v117p5179 "The periodicity of the torsion. A negative
>> value is not used in the calculation but signifies more than one component
>> around a given bond."  I don't know what is the role of the parameters in
>> line with negative periodicity. I am trying to find the corresponding code
>> in src/ but failed to understand so many formal parameters in the
>> subroutines...
>
>This has to do with telling leap that it should look for additional torsion
>terms for a given set of atom types. From http://ambermd.org/formats.html
>
>PN         The periodicity of the torsional barrier.
>                    NOTE: If PN .lt. 0.0 then the torsional potential
>                          is assumed to have more than one term, and the
>                          values of the rest of the terms are read from the
>                          next cards until a positive PN is encountered.
>The
>                          negative value of pn is used only for identifying
>                          the existence of the next term and only the
>                          absolute value of PN is kept.
>
>I'm not entirely sure if leap strictly follows this though (I believe that
>it might just look for all dihedral entry types and this really only
>mattered in the days before leap but I might be wrong - a simple test would
>be to check).
>
>> The parameterized torsional constants for sulfonium group are:
>> -----
>> Torsional Interaction (Kcal/mol)
>>                           V1/2         V2/2         V3/2
>> SP ¨C CT ¨C CT ¨C CT     -1.6814       1.0698        -0.0001
>> SP ¨C CT ¨C CT ¨C H1      0.9529       1.1047        0.0695
>> SP ¨C CT ¨C CT ¨C O3      3.5661       0.5502        -0.0208
>> ----------
>> 
>> Any one who can give me some suggestions on how to use these parameters in
>> AMBER10?
>
>In this case you have 3 torsion terms, I assume corresponding to a 1 fold, 2
>fold and 3 fold term. The /2 here corresponds to the Vn/2 yes? I believe
>AMBER expects Vn/2 to be specified in the frcmod file and not Vn given the
>following:
>
>http://ambermd.org/formats.html
>
>                           (PK/IDIVF) * (1 + cos(PN*phi - PHASE))
>
>         PK         The barrier height divided by a factor of 2.
>
>
>So assuming the phase is zero you should probably write your frcmod file as
>follows:
>
>SP ¨C CT ¨C CT ¨C CT     1  -0.0001   0.0  -3
>SP ¨C CT ¨C CT ¨C CT     1   1.0698   0.0  -2
>SP ¨C CT ¨C CT ¨C CT     1  -1.6814   0.0   1
>SP ¨C CT ¨C CT ¨C H1     1   0.0695   0.0  -3
>
>etc.
>
>To double check things though I would encourage you to make a prmtop
>containing just your sulfonium group. Then load this into rdparm and issues
>printdihedrals. This will give you a list of all the dihedrals so you can
>manually check that they are all present.
>
>All the best
>Ross
>
>
>/\
>\/
>|\oss Walker
>
>| Assistant Research Professor |
>| San Diego Supercomputer Center |
>| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk | 
>| http://www.rosswalker.co.uk | PGP Key available on request |
>
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