AMBER Archive (2005)

Subject: AMBER: my prepin file in lowe-case

From: Vijay Manickam Achari (vjrajamany_at_yahoo.com)
Date: Tue May 24 2005 - 02:51:55 CDT

Dear amber users
I have modeled residue called thio-glucoside.

In my prepin file, the atom type is in lowe-case
correspond with gaff.dat file.

I didnt change the atom type to Upper-case.

But my residue shows no problem.

Due to the lower-case, will be there any problem in
future, like in xx.top or xx.crd files?
Since I am new to Amber I would like to know this at
earlier stage to avoid any accidents later.

Thanks
Vijay

--- Ilyas Yildirim <yildirim_at_pas.rochester.edu> wrote:
> Dear Vijay,
>
> You have to write down all those missing parameters
> by hand. It seems that
> parmchk could not find any known force field
> parameter for those atom
> types defined in your .frcmod file. Find a structure
> which looks very
> similar to your structure, and define the atom types
> by comparing them.
> Otherwise, you have to find/measure/calculate those
> missing parameters by
> yourself by doing some experiments/simulations
> (which I assume is not
> what you want).
>
> What I mean by a SIMILAR structure is the following:
> For instance load the
> RU and RC structures in xleap. And edit the RC and
> RU structures
> seperatrely (in different windows). Click on DISPLAY
> > Types.
>
> You will see the atom types defined for individual
> atoms. If you compare
> both of the structures, you will see that the atom
> types for the sugar
> part is exactly the same, H6 atoms have an atom type
> 'H4', C5 and C6 have
> atom types of 'CM', and so on...
>
> So, by comparison, you can define most of the
> missing atom types of your
> system. If there isnt any other reasonable estimate
> for some of the atoms
> in your system, u have to find a good estimate for
> that missing atoms.
> For instance, if an O is bonded to a C in a ring, in
> the AMBER force
> field, the Carbond has an atom type of "C" and the
> oxygen has an atom type
> of "O". The same thing can be done for -NH2. So, try
> to find a good
> estimate for those missing parameters.
>
> Good luck,
>
> On Tue, 24 May 2005, Vijay Manickam Achari wrote:
>
> > Dear amber users I have used the command as below
> to
> > generate frcmod file.
> > > parmchk -i xx.prepin -f prepi -o xx.frcmod
> >
> > I do get file as xx.frcmod,
> > but it seems there are many lines which contains
> no
> > value. It stated as "require your attention".
> >
> > I have attached the xx.frcmod file together with
> this
> > mail.
> >
> > HOw to handle this problem than and since I am
> using
> > glycam04 force field, how to use that information
> to
> > create frcmod file
> >
> > Thanks
> >
> > Vijay
> >
> >
> >
> >
> >
> >
>
___________________________________________________________
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>
> --
> Ilyas Yildirim
>
>
---------------------------------------------------------------
> - Department of Chemisty - -
> - University of Rochester - -
> - Hutchison Hall, # B10 - -
> - Rochester, NY 14627-0216 - Ph.:(585) 275 67
> 66 (Office) -
> - http://www.pas.rochester.edu/~yildirim/ -
>
>
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