Re: AMBER: Can GB and MS work correctly together in mmpbsa?

From: Holger Gohlke <gohlke.bioinformatik.uni-frankfurt.de>
Date: Fri, 15 Jul 2005 07:39:21 +0200

Am Freitag, 15. Juli 2005 04:38 schrieb zhli_2000.126.com:
> Hi, all
> Because there is an atom F in the ligand, mmpbsa cann't be calculated
> correctly only using DC,MM and GB. So I add its atom radium in the
> mm_pbsa_calceneent.pm file and run the calculation using DC, MM, GB and MS.
> But I meet the new error.
>
> The input file and error message is the following:
> --------------------------------------------------------------------
> PREFIX min_cyc16
> PATH ./
> #
> COMPLEX 1
> RECEPTOR 1
> LIGAND 1
> #
> COMPT ./mincomplex.top
> RECPT ./ppo.top
> LIGPT ./cyc16.top
> #
> GC 0
> AS 0
> DC 1
> #
> MM 1
> GB 1
> PB 0
> MS 1
> #
> NM 0
> #
> -------------------------------------------------------------------
> The error message is :
> Checking sanity
> Checking GENERAL
> Energy decomp is not (yet) possible with GC, AS, NM, PB, MS

If you switch MS=1 to MS=0, it should work. Energy decomposition does not work
so far with a SAS calculation based on MS, but relies on another method
approximating atomic surfaces starting from icosahedra.
 
Best regards

Holger

>
>
> What shall I do to deal with it? Thank you very much!
>
>
> zhang
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

-- 
++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Holger Gohlke
J.W. Goethe-Universitaet
Fachbereich Biologie und Informatik
Institut fr Mikrobiologie
Marie-Curie-Str. 9
60439 Frankfurt/Main
Germany
Tel.:  (+49) 69-798-29411; Fax: (+49) 69-798-29826
Email: gohlke.bioinformatik.uni-frankfurt.de
URL:   http://www.uni-frankfurt.de/~hgohlke
++++++++++++++++++++++++++++++++++++++++++++++++++
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Jul 15 2005 - 06:53:01 PDT
Custom Search