since the documentation says that -3- is not used, many files do not include
it.
same with section -8-, many files do not use explicit H-bond terms.
On Mon, Mar 15, 2010 at 8:32 PM, <whimsica.aol.com> wrote:
>
> No Attitude here. Just the opposite. I greatly appreciate the help.
> Sorry if it didn't seem that way. I'm excited that I got 1 out of 6 of the
> parts I need
> to make something happen.
>
> Are you saying the page is organized in order? If so that's the main piece
> of information I needed.
>
>
> for example in parm99.dat
> C 12.01 0.616 ! sp2 C carbonyl group
> CA 12.01 0.360 sp2 C pure aromatic (benzene)
> CB 12.01 0.360 sp2 aromatic C, 5&6 membered ring
> junctio
>
> transitions to
>
> C H HO N NA NB NC N2 NT N2 N3 N* O OH OS P O2
> OW-HW 553.0 0.9572 ! TIP3P water
> HW-HW 553.0 1.5136 TIP3P water
> C -C 310.0 1.525 Junmei et al, 1999
>
> Didn't -3- get skipped.
>
> Thanks again,
>
> Dan
>
> Here's what I'm looking at now.
>
>
> - 1 - ITITL
>
> FORMAT(20A4)
>
> ITITL A title for identification of the parameter set.
>
>
> ------------------------------------------------------------------------
>
> - 2 - ***** INPUT FOR ATOM SYMBOLS AND MASSES *****
>
> KNDSYM , AMASS, ATPOL
>
> FORMAT(A2,2X,F10.2x,f10.2)
>
> KNDSYM The unique atom symbol used in the system.
>
> AMASS Atomic mass of the center having the symbol "KNDSYM".
>
> ATPOL The atomic polarizability for each atom (in A**3)
> This is the type of polarizability used in sander
> and gibbs. No parameters are supplied for this since
> the feature is still in development (Amber 4.1).
>
> NOTE: All the unique atomic symbols and their masses must
> be read. The input is terminated by a blank card.
>
>
>
> ------------------------------------------------------------------------
>
> - 3 - ***** INPUT FOR ATOM SYMBOLS THAT ARE HYDROPHILIC *****
>
> JSOLTY(I)
>
> FORMAT(20(A2,2X))
>
> JSOLTY(I) The atom symbols which are hydrophilic in solution.
> This information is read but not used.
>
> The input is terminated when a blank value is read for
> the atom symbol.
>
>
> ------------------------------------------------------------------------
>
> - 4 - ***** INPUT FOR BOND LENGTH PARAMETERS *****
>
> IBT , JBT , RK , REQ
>
> FORMAT(A2,1X,A2,2F10.2)
>
> IBT,JBT Atom symbols for the two bonded atoms.
>
> RK The harmonic force constant for the bond "IBT"-"JBT".
> The unit is kcal/mol/(A**2).
>
> REQ The equilibrium bond length for the above bond in
> angstroms
>
> The input is terminated by a blank card.
>
>
>
>
> Dan
>
>
>
>
>
>
>
>
> -----Original Message-----
> From: Bill Ross <ross.cgl.ucsf.edu>
> To: amber.ambermd.org
> Sent: Mon, Mar 15, 2010 5:05 pm
> Subject: Re: [AMBER] Can anyone tell me what the parm99.dat values
> correspond to?
>
>
> > Okay now the first term of the wikipedia amber force is accounted
> for...i=
> > e Bonds.
> >
> > What about all the other parameters necessary to compute angles,
> torsions,=
> > electrostatics and vanderwalls?
>
> If you read the rest of parm.dat format, you should be able to
> figure this out.
>
> > And how did you know that=20
> > parm99.dat was for Bonds? There is nothing to suggest that in the file
> its=
> > elf.
>
> The documentation says so.
>
> > There is no header before it starts listing values. I'm just looking at
> th=
> > e file
> > opening it with a text editor. Are you looking at it with a different
> meth=
> > od?
> >
> > Thanks and keep the info coming 1/6 accounted for now.
>
> I'm done, good luck with that attitude.
>
> Bill
>
> > IBT,JBT Atom symbols for the two bonded atoms.
> >
> > RK The harmonic force constant for the bond "IBT"-"JBT".
> > The unit is kcal/mol/(A**2).
> >
> > REQ The equilibrium bond length for the above bond in
> angs=
> > troms
> >
> > The input is terminated by a blank card.
> >
> >
> > See if you can generalize from that to understand the rest of parm.dat
> > format.
> >
> > Bill
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > =20
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 15 2010 - 18:30:02 PDT
