Hi Xuegin,
Sorry for the delayed answer.
Did you clean up the directory before rerunning mm_pbsa.pl?
This is needed because mm_pbsa.pl doesn't overwrite old output files. Insted it appends the new output at existing files.
Subsequently mm_pbsa_statistics.pl gets confused.
That means, you need to remove all output files before rerunning mm_pbsa.pl.
I guess that could be the reason for this problem.
Cheers!
Hannes
-------- Original-Nachricht --------
> Datum: Tue, 19 Jan 2010 22:07:39 +0800 (CST)
> Von: xueqin pang <pangxueqintea.yahoo.com.cn>
> An: AMBER Mailing List <amber.ambermd.org>
> Betreff: Re: [AMBER] problem with DC of mmgbsa
> Hannes,
>
> It works. Thanks so much for your help.
>
> And a new problem is : when mmpbsa run with ligand to get * _lig.all.out
> , I get the error: Missing BELE for MM in 1 ( residue 1)
>
> do you have any suggestions on this problem.
> or, it is just alright when ligand the only one molecular ?
>
> Thanks again
>
> Xueqin
>
>
> --- 10年1月19日，周二, Hannes Kopitz <Hannes.Kopitz.gmx.de>
> 写道：
>
>
> 发件人: Hannes Kopitz <Hannes.Kopitz.gmx.de>
> 主题: Re: [AMBER] problem with DC of mmgbsa
> 收件人: "AMBER Mailing List" <amber.ambermd.org>
> 日期: 2010年1月19日,周二,上午4:24
>
>
> Hello Xueqin,
>
> Please try 309-309 instead of 309 and 1-1 instead of 1.
>
> Cheers!
> Hannes
>
> -------- Original-Nachricht --------
> > Datum: Mon, 18 Jan 2010 10:23:45 +0800 (CST)
> > Von: xueqin pang <pangxueqintea.yahoo.com.cn>
> > An: amber mail list <amber.ambermd.org>
> > Betreff: [AMBER] problem with DC of mmgbsa
>
> > Hello everyone,
> >
> > When doing gb-mm-dc I always get the error: Wrong format for decomp: 309
> > (which is my ligand). And so it stopped when check dc. However, if only
> do
> > gb-mm, it is ok.
> >
> > I have tried different system and the same error occurred. I have also
> > check prmtop and _lig.crd with vmd, it is ok.
> >
> > So what is the possible reasons for this and do you have any
> suggestions?
> >
> > Thanks so much
> >
> > Xueqin
> >
> > error: Wrong format for decomp: 309
> >
> > ###########################################################
> > # Input parameters for mm_pbsa.pl
> > #
> > # Holger Gohlke
> > # 08.01.2002
> > #
> > #####################################################
> > .GENERAL
> > #
> > VERBOSE 0
> > #
> > PREFIX E169-A
> > PATH ./
> > START 1
> > STOP 5
> > OFFSET 1
> > #
> > COMPLEX 1
> > RECEPTOR 1
> > LIGAND 1
> > #
> > COMPT ../E169-A.prmtop
> > RECPT ../E169.prmtop
> > LIGPT ../A.prmtop
> > #
> > GC 0
> > AS 0
> > DC 1
> > #
> > MM 1
> > GB 1
> > PB 0
> > MS 0
> > #
> > NM 0
> > #
> > #############################################################
> > .DECOMP
> > #
> > DCTYPE 4
> > #
> > COMREC 1-308
> > COMLIG 309
> > COMPRI 1-309
> > RECRES 1-308
> > RECPRI 1-308
> > RECMAP 1-308
> > LIGRES 1
> > LIGPRI 1
> > LIGMAP
> > 3###############################################################
> > .MM
> > #
> > DIELC 1.0
> > #
> > ################\###############################################
> > .GB
> > #
> > IGB 2
> > GBSA 2
> > SALTCON 0.00
> > EXTDIEL 78.50
> > INTDIEL 1.0
> > #
> > SURFTEN 0.0072
> > SURFOFF 0.00
> > #
> > ################################################################
> > .MAKECRD
> > #
> > BOX no
> > NTOTAL 32664
> > NSTART 1
> > NSTOP 5
> > NFREQ 1
> > NUMBER_LIG_GROUPS 1
> > LSTART 4887
> > LSTOP 4926
> > NUMBER_REC_GROUPS 2
> > RSTART 1
> > RSTOP 4886
> > RSTART 4927
> > RSTOP 32664
> > #
> > #########################################################
> > #
> > TRAJECTORY ../../../../E169-A.mdcrd.gz
> > ##########################################################
> >
> >
> >
> > ___________________________________________________________
> > 好玩贺卡等你发，邮箱贺卡全新上线！
> > http://card.mail.cn.yahoo.com/
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> GRATIS für alle GMX-Mitglieder: Die maxdome Movie-FLAT!
> Jetzt freischalten unter http://portal.gmx.net/de/go/maxdome01
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> ___________________________________________________________
> 好玩贺卡等你发，邮箱贺卡全新上线！
> http://card.mail.cn.yahoo.com/
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Jetzt kostenlos herunterladen: Internet Explorer 8 und Mozilla Firefox 3.5 -
sicherer, schneller und einfacher! http://portal.gmx.net/de/go/chbrowser
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 22 2010 - 08:00:02 PST
