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--- 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 – CT – CT – CT -1.6814 1.0698 -0.0001 >> SP – CT – CT – H1 0.9529 1.1047 0.0695 >> SP – CT – CT – 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 – CT – CT – CT 1 -0.0001 0.0 -3 >SP – CT – CT – CT 1 1.0698 0.0 -2 >SP – CT – CT – CT 1 -1.6814 0.0 1 >SP – CT – CT – 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.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.scripps.edu >To unsubscribe, send "unsubscribe amber" (in the *body* of the email) > to majordomo.scripps.edu >. �����������������������������������������������������������岫����'鼩唺� ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to amber.scripps.edu To unsubscribe, send "unsubscribe amber" (in the *body* of the email) to majordomo.scripps.eduReceived on Fri Dec 05 2008 - 17:59:48 PST