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
> ##########################################################
>
>
>
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Received on Tue Jan 19 2010 - 06:30:02 PST
