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Error after generating the protein membrane complex
#38170 01/21/21 01:02 PM
Joined: Jan 2021
Posts: 11
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Rakesh Offline OP
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I have generated a protein membrane complex and after viewing the out file i can see the below errror. will it effect my simulation, what does the below script means?


PARAMETER FILE BEING READ FROM UNIT 98
RDTITL> * SYNTHETIC POLYMER PARAMETER
RDTITL> *
PARRDR> Error: Repeated BOND parameter ( 432): CG1N CG32 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1180): CG32 CG1N NG1T is replaced
PARRDR> Error: Repeated ANGLE parameter ( 2090): CG2D CG32 NG31 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1960): CG2O CG31 CG33 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1232): CG33 CG2D CG33 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 2080): CG1N CG32 HGA2 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 2012): CG32 CG31 OG30 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 2894): CG32 NG31 CG33 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1964): CG2O CG31 OG31 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1974): CG2O CG31 OG31 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1958): CG2O CG31 CG31 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1984): CG2R CG31 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6418): CG32 CG32 CG32 NG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6418): CG32 CG32 CG32 NG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3818): OG31 CG2O CG31 NG2S is replaced
PARRDR> Error: Repeated DIHE parameter ( 7125): HGA3 CG33 NG31 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 2991): CG33 CG2D CG33 HGA3 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6440): CG33 CG32 CG32 NG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6440): CG33 CG32 CG32 NG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6060): OG30 CG31 CG32 HGA2 is replaced
PARRDR> Error: Repeated DIHE parameter ( 2934): CG2D CG2D CG32 NG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 2935): CG2D CG2D CG32 NG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3807): OG30 CG2O CG31 CG33 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6731): CG2D CG32 NG31 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6732): CG2D CG32 NG31 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6733): CG2D CG32 NG31 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6731): CG2D CG32 NG31 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6732): CG2D CG32 NG31 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6733): CG2D CG32 NG31 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6731): CG2D CG32 NG31 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6732): CG2D CG32 NG31 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6733): CG2D CG32 NG31 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6327): CG2D CG32 CG32 CG2D is replaced
PARRDR> Error: Repeated DIHE parameter ( 6328): CG2D CG32 CG32 CG2D is replaced
PARRDR> Error: Repeated DIHE parameter ( 6737): CG2D CG32 NG31 HGPA is replaced
PARRDR> Error: Repeated DIHE parameter ( 3796): OG2D CG2O CG31 CG33 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6058): OG30 CG31 CG32 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6059): OG30 CG31 CG32 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6058): OG30 CG31 CG32 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6059): OG30 CG31 CG32 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6780): HGA2 CG32 NG31 CG33 is replaced
PARRDR> Error: Repeated DIHE parameter ( 2978): HGA4 CG2D CG32 NG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6116): CG2O CG31 CG33 HGA3 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3805): OG30 CG2O CG31 CG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6228): CG2R CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6229): CG2R CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6230): CG2R CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6228): CG2R CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6229): CG2R CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6230): CG2R CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6228): CG2R CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6229): CG2R CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6230): CG2R CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3900): OG2D CG2O CG31 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5935): CG32 CG31 CG31 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3810): OG30 CG2O CG31 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3811): OG30 CG2O CG31 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5937): CG33 CG31 CG31 CG33 is replaced
PARRDR> Error: Repeated DIHE parameter ( 2936): CG2D CG2D CG32 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 2937): CG2D CG2D CG32 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 2938): CG2D CG2D CG32 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 2936): CG2D CG2D CG32 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 2937): CG2D CG2D CG32 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 2938): CG2D CG2D CG32 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 2936): CG2D CG2D CG32 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 2937): CG2D CG2D CG32 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 2938): CG2D CG2D CG32 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6222): CG2O CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6223): CG2O CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6224): CG2O CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6222): CG2O CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6223): CG2O CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6224): CG2O CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6222): CG2O CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6223): CG2O CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6224): CG2O CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6219): CG2O CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6220): CG2O CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6221): CG2O CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6219): CG2O CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6220): CG2O CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6221): CG2O CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6219): CG2O CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6220): CG2O CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6221): CG2O CG31 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5909): CG2O CG31 CG31 CG33 is replaced
PARRDR> Error: Repeated DIHE parameter ( 2968): CG33 CG2D CG32 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 2969): CG33 CG2D CG32 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 2970): CG33 CG2D CG32 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3815): OG31 CG2O CG31 CG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3820): OG31 CG2O CG31 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5908): CG2O CG31 CG31 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3794): OG2D CG2O CG31 CG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5913): CG2O CG31 CG31 HGA1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3800): OG2D CG2O CG31 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 4935): CG2R CG2R CG31 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 6008): CG31 CG31 CG32 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5941): CG33 CG31 CG31 OG31 is replaced
PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.

CHARMM> RETURN
VCLOSE: Closing unit 98 with status "KEEP"

RETURNING TO INPUT STREAM 99

Re: Error after generating the protein membrane complex
Rakesh #38173 01/21/21 05:10 PM
Joined: Sep 2003
Posts: 8,532
Likes: 2
rmv Offline
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Posts: 8,532
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The latest CHARMM-GUI scripts use every possible topology and parameter file, whether they are actually needed or not, despite that fact that there may be duplicated entries.

Questions about CHARMM-GUI are best directed to their web site


Rick Venable
computational chemist


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