AMBER Archive (2005)

Subject: Re: AMBER: my frcmod file created using parmchk

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Mon May 23 2005 - 23:03:42 CDT

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
>
>
>
>
>
> ___________________________________________________________
> Yahoo! Messenger - NEW crystal clear PC to PC calling worldwide with voicemail http://uk.messenger.yahoo.com 

-- 
  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/			-
  ---------------------------------------------------------------

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu