[AMBER] mmpbsa-problem

From: Dima A Sabbah <dsabbah.unmc.edu>
Date: Fri, 9 Apr 2010 11:30:59 -0500

Hi Dear,

   We got this message when we did mm-pbsa although= we downloaded the bugfix
   script for Amber 10 and the problem still e= xisted.Would you please let me
   know the solution?
   Use of uninitialized value in multiplication (*) at /usr/local/amber10/ src/mm_pbsa/mm_pbsa_statistics.pm line 1423.
   Use of uninitialized value in multiplication (*) at /usr/local/ambe r10/src/mm_pbsa/mm_pbsa_statistics.pm line 1542.
   Regard= s,

   -----amber-bounces.amberm= d.org wrote: -----

     To: "'AMBER Mailing List'" <amber.ambermd.org>
     From: "= Ross Walker" <ross.rosswalker.co.uk>
     Sent by: amber-bounces.amberm= d.org
     Date: 04/09/2010 12:54AM
     Subject: RE: [AMBER] multiconformation= al RESP fitting with antechamber
     Hi Miranda,
     I was not aware tha= t antechamber can do multiple conformational fits, or
     even multi-orienta= tional fits and I have certainly never tried it.
     the program R.E= .D. is capable of doing this and more so you may want to
     consider using = that to do your multi-conformational runs.
     All the best
> -----Original Message-----
     = > From: amber-bounces.ambermd.org [[2]mailto:amber-bounces.ambermd.org]
> Beh= alf Of Yi Shang
> Sent: Thursday, April 08, 2010 12:28 PM
> To:= amber.ambermd.org
> Subject: [AMBER] multiconformational RESP fittin= g with antechamber
> Dear All,
> Single conformational= RESP fitting was done nicely with antechamber
> using
> comman= d like:
> `antechamber -i g98.out -fi gout -o sustiva_resp.mol2 -fo= mol2 -c
> In Amber tools 1.3 manual it wasn't clear if multi-c= onformational RESP
> fitting is doable directly using antechamber. Ho= wever, it says the
> following: "Starting with Amber 10, the program = (respgen, a program
> called
> by antechamber) supports a singl= e molecule with one or multiple
> conformations RESP fittings." = ;I wasn't able to figure out how, with
> information provided.
>= ; Could anyone that has done multi-conformational RESP fitting this way
     = > give
> me some clue here?
> Thank you!
> --
> = Miranda
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Received on Fri Apr 09 2010 - 10:00:04 PDT
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