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 每 CT 每 CT 每 CT -1.6814 1.0698 -0.0001 >> SP 每 CT 每 CT 每 H1 0.9529 1.1047 0.0695 >> SP 每 CT 每 CT 每 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 每 CT 每 CT 每 CT 1 -0.0001 0.0 -3 >SP 每 CT 每 CT 每 CT 1 1.0698 0.0 -2 >SP 每 CT 每 CT 每 CT 1 -1.6814 0.0 1 >SP 每 CT 每 CT 每 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 | > >Note: Electronic Mail is not secure, has no guarantee of delivery, may not >be read every day, and should not be used for urgent or sensitive issues. > > > > >----------------------------------------------------------------------- >The AMBER Mail Reflector >To post, send mail to amber_at_scripps.edu >To unsubscribe, send "unsubscribe amber" (in the *body* of the email) > to majordomo_at_scripps.edu >. 廑'f ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber_at_scripps.edu To unsubscribe, send "unsubscribe amber" (in the *body* of the email) to majordomo_at_scripps.edu