AMBER Archive (2004)

Subject: Re: AMBER: Do we have to optimize the structure in order to do MEP Calculations?

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Tue Apr 20 2004 - 18:42:34 CDT

Dear Mr. Case,

antechamber converted the .pdb file to a .mol2 file correctly. I did not
start on the MEP calculations yet, but I am sure it will work fine. Thanks
for your help.

Best, 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       - Home Address:                -
  - University of Rochester      -                              -
  - Hutchison Hall, Office B10   - 60 Crittenden Blvd. Apt. 232 -
  - Rochester, NY 14627-0216     - Rochester, NY 14620          -
  - Ph.:(585) 275 20 31 (Office) - Ph.:(585) 242 91 37 (Home)   -
  - Homepage: http://www.pas.rochester.edu/~yildirim/           -
  ---------------------------------------------------------------

On Tue, 20 Apr 2004, David A. Case wrote:

> On Tue, Apr 20, 2004, Ilyas Yildirim wrote:
> > Here is the content of the pdb file I am using:
> >
> > ATOM      1  C1  UNK 0   1      -7.625   2.311   2.861  1.00  0.00
> > ATOM      2  C2  UNK 0   1      -6.591   3.639   1.072  1.00  0.00
> > ATOM      3  C3  UNK 0   1      -7.828   0.195   3.843  1.00  0.00
>
> OK, there is a bug in antechamber, in that is fails to recognize correctly
> the chainID (column 22).  As a workaround, replace the "0" after UNK above
> with a space, and re-run.  I will post a bugfix later today.
>
> Thanks for reporting this.
>
> ...regards...dac
>
>

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