AMBER Archive (2009)

Subject: Re: [AMBER] Problems with MM-PBSA Calculation after MD

From: Hannes Kopitz (Hannes.Kopitz_at_gmx.de)
Date: Thu Mar 12 2009 - 06:06:54 CDT

Dear German,

Seems like you simply used the wrong prmtop-file. You need a prmtop-file w/o any box information since the energy calculation is done w/o periodic boundary conditions.

Cheers!
Hannes Kopitz

University of Kiel
Germany

-------- Original-Nachricht --------
> Datum: Thu, 12 Mar 2009 10:28:23 +0100
> Von: German Erlenkamp <german.erlenkamp_at_pharmazie.uni-halle.de>
> An: Amber User <amber_at_ambermd.org>
> Betreff: [AMBER] Problems with MM-PBSA Calculation after MD

> Dear Amber-Users,
>
> I've got a problem with the MM-PBSA calculation after my MD.
> Here is the output with the error-message:
>
> BOX TYPE: TRUNCATED OCTAHEDRON
>
> --------------------------------------------------------------------------------
> 2. CONTROL DATA FOR THE RUN
> --------------------------------------------------------------------------------
>
>
>
> General flags:
> imin = 1, nmropt = 0
>
> Nature and format of input:
> ntx = 1, irest = 0, ntrx = 1
>
> Nature and format of output:
> ntxo = 1, ntpr = 50, ntrx = 1,
> ntwr = 500, iwrap = 0, ntwx = 0,
> ntwv = 0, ntwe = 0, ioutfm = 0,
> ntwprt = 0, idecomp = 0, rbornstat= 0
>
> Potential function:
> ntf = 1, ntb = 0, igb = 2,
> nsnb = 99999, ipol = 0, gbsa = 0,
> iesp = 0, dielc = 1.00000, cut= 999.00000,
> intdiel = 1.00000, saltcon = 0.00000, offset = 0.09000,
> gbalpha= 0.80000, gbbeta = 0.00000, gbgamma = 2.90912,
> surften = 1.00000, rdt = 0.00000, rgbmax = 25.00000,
> alpb = 0, scnb = 2.00000, scee = 1.20000,
>
> Frozen or restrained atoms:
> ibelly = 0 , ntr = 0
>
> Energy minimization:
> maxcyc = 1, ncyc = 0, ntmin = 1,
> dx0 =0.01000, drms = 0.00010
>
> Error: ifbox=2 in prmtop but angles are not correct
>
> *** input error(s)
>
> The 'input error(s)' message is my problem.
>
> The funny thing is: a few weeks ago I made the same MD and everything
> works fine.
>
> Does somebody know how to solve the problem?
>
> Thanks in advance.
>
> Best regards
>
> German
>
> --
> German Erlenkamp
> Institut fuer Pharmazeutische Chemie
> Martin-Luther-Universitaet Halle
> Wolfgang-Langenbeck-Str.4
> 06120 Halle/ Saale
>
> E-Mail: german.erlenkamp_at_pharmazie.uni-halle.de
> Phone: (49)345 - 55 25 043
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber 

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