Yes, you will need to add in the bromine parameters to
$AMBERHOME/src/sander/mdread.f as mentioned in this previous post (
http://archive.ambermd.org/201111/0370.html) and re-compile sander
afterwards.
I hope that helps.
-Bill
On Sun, May 20, 2012 at 10:30 PM, marawan hussain
<marawanhussain.yahoo.com>wrote:
> 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
>
--
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
Received on Sun May 20 2012 - 20:00:03 PDT
