HI Bill,
Several outputs have been written, but i figured out this error:
END
END
bad atom type: br
in the (_MMPBSA_gb_decomp_com.mdin) file..
Do i need to recompile sander as i have read in similar posts.....???
Regards
Marawan
________________________________
From: Bill Miller III <brmilleriii.gmail.com>
To: marawan hussain <marawanhussain.yahoo.com>; AMBER Mailing List <amber.ambermd.org>
Sent: Monday, 21 May 2012 12:14 PM
Subject: Re: [AMBER] MMPBSA-CalcError
What mdout files were written? I assume at least _MMPBSA_complex*mdout was
written. What is printed at the end of that file? Is there an error message
in one of the mdout files?
-Bill
On Sun, May 20, 2012 at 10:00 PM, marawan hussain
<marawanhussain.yahoo.com>wrote:
> Dear AMBER 12 User,
> I'm trying to do an MMPBSA.py calculation of a ligand/protein complex but
> i got this error:
> CalcError: /apps/amber/12/bin/sander failed with prmtop com_m19.top!
> Exiting. All files have been retained.
>
>
> I don't think there is a problem in the installation as a very similar
> complexes have been done successfully..
> When i remove the decomposition option and rerun again the calculation
> goes fine, i use the following input:\
> Input file for running PB and GB
> &general
> startframe=1, endframe=2, verbose=1 (2 frames for testing only)
> # entropy=1,
> /
> &gb
> igb=5, saltcon=0.100
> /
> &decomp
> idecomp=1, print_res="320; 18-19; 26-27; 43-45; 47; 63; 66; 69; 74-77;
> 88; 90-97; 128;133; 141-142; 144; 153-158; 298; 301-302", csv_format=0
> /
>
> I have read a similar post but i couldn't identify a final solution...
> King regards
> Marawan
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun May 20 2012 - 20:00:03 PDT
