AMBER Archive (2006)

Subject: Re: AMBER: lib file

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Fri Feb 03 2006 - 19:11:36 CST

Dear Snoze,

These messages mean that the necessary parameters to describe your system
are missing. I just checked out the HEM structure I gave to u, and they
work fine. I would say that your .pdb file has some atom types which needs
the given parameter informations. For instance, the angle parameter

HS - SH - FE

is missing. You need to give these missing parameter info.s using an
frcmod file, like the one I sent to u, which is prepared for the HEM
structure. Describing these parameters is very hard, if there is not any
described in the literature. What is your .pdb file? Is it purely made of
aminoacids and/or nucleicacids?

On Fri, 3 Feb 2006, snoze pa wrote:

> Hi Ilya and Amber community,
> thanks a lot for your help. I am able to fix so much in my system. But when
> I am loading HEM prameter, it is giving me following message.
> Any idea about this. How can recover from this message. Is it because of
> ATOM in my PDB and HEME parameter file or something else.
>
> Could not find bond parameter for: SH - FE
> Checking for angle parameters.
> Could not find angle parameter: HS - SH - FE
> Could not find angle parameter: SH - FE - NP
> Could not find angle parameter: SH - FE - NO
> Could not find angle parameter: SH - FE - NP
> Could not find angle parameter: SH - FE - NO
> Could not find angle parameter: CT - SH - FE
> There are missing parameters.
> check: Warnings: 40
>
> thanks in advance
> snoze
> 

-- 
  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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