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*phiphase)  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,
>
>
>> CTCTN C 1 0.50 180.0 4. phi,psi,parm94
>> CTCTN C 1 0.15 180.0 3. phi,psi,parm94
>> CTCTN C 1 0.00 0.0 2.
>> JCC,7,(1986),230
>> CTCTN 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 
>
>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
>.
ÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿÿá¶Úÿÿ÷'þf¢—üš†Šÿ

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
