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
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>
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Received on Mon Mar 15 2010 - 18:00:02 PDT
