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#37678 - 10/29/19 04:31 AM Repeated BOND parameter ( 482): CG2D CG2D is replaced
vht Offline
Forum Member

Registered: 10/24/19
Posts: 6
Hi all,

The system that I am currently working on contains a protein with two ligands.For the ligands,.prm and .rtf files are generated from the C-GUI.But following error was there in the output file.

CHARMM> open read card unit 20 name ret/ret.prm
OPNLGU> Unit already open. The old file will be closed first.
VCLOSE: Closing unit 20 with status "KEEP"
VOPEN> Attempting to open::ret/ret.prm::
OPNLGU> Unit 20 opened for READONLY access to ret/ret.prm

CHARMM> read para flex card unit 20 append

PARAMETER FILE BEING READ FROM UNIT 20
TITLE> * PARAMETERS GENERATED BY ANALOGY BY
TITLE> * CHARMM GENERAL FORCE FIELD (CGENFF) PROGRAM VERSION 2.2.0
TITLE> *
PARRDR> Error: Repeated BOND parameter ( 482): CG2D CG2D is replaced
PARRDR> Error: Repeated BOND parameter ( 483): CG2D CG2D is replaced
PARRDR> Error: Repeated BOND parameter ( 495): CG2D HGA4 is replaced
PARRDR> Error: Repeated BOND parameter ( 497): CG2D CG2D is replaced
PARRDR> Error: Repeated BOND parameter ( 504): CG2D CG30 is replaced
PARRDR> Error: Repeated BOND parameter ( 505): CG2D CG32 is replaced
PARRDR> Error: Repeated BOND parameter ( 506): CG2D CG33 is replaced
PARRDR> Error: Repeated BOND parameter ( 509): CG2D HGA4 is replaced
PARRDR> Error: Repeated BOND parameter ( 716): CG30 CG32 is replaced
PARRDR> Error: Repeated BOND parameter ( 717): CG30 CG33 is replaced
PARRDR> Error: Repeated BOND parameter ( 753): CG32 CG32 is replaced
PARRDR> Error: Repeated BOND parameter ( 770): CG32 OG31 is replaced
PARRDR> Error: Repeated BOND parameter ( 784): CG32 HGA2 is replaced
PARRDR> Error: Repeated BOND parameter ( 824): CG33 HGA3 is replaced
PARRDR> Error: Repeated BOND parameter ( 946): OG31 HGP1 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1273): CG2D CG2D CG2D is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1280): CG2D CG2D HGA4 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1285): CG2D CG2D HGA4 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1310): CG2D CG2D CG2D is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1312): CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1313): CG2D CG2D CG33 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1315): CG2D CG2D HGA4 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1320): CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1321): CG2D CG2D CG32 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1322): CG2D CG2D CG33 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1323): CG2D CG2D HGA4 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1337): CG32 CG2D CG33 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1338): CG32 CG2D HGA4 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1799): CG2D CG30 CG32 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1800): CG2D CG30 CG33 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1808): CG32 CG30 CG33 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1810): CG33 CG30 CG33 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1938): CG2D CG32 CG32 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1939): CG2D CG32 OG31 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1941): CG2D CG32 HGA2 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1987): CG30 CG32 CG32 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 1989): CG30 CG32 HGA2 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 2008): CG32 CG32 CG32 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 2024): CG32 CG32 HGA2 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 2072): OG31 CG32 HGA2 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 2087): HGA2 CG32 HGA2 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 2133): CG2D CG33 HGA3 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 2143): CG30 CG33 HGA3 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 2174): HGA3 CG33 HGA3 is replaced
PARRDR> Error: Repeated ANGLE parameter ( 2695): CG32 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3151): CG2D CG2D CG2D CG2D is replaced
PARRDR> Error: Repeated DIHE parameter ( 3152): CG2D CG2D CG2D CG2D is replaced
PARRDR> Error: Repeated DIHE parameter ( 3151): CG2D CG2D CG2D CG2D is replaced
PARRDR> Error: Repeated DIHE parameter ( 3152): CG2D CG2D CG2D CG2D is replaced
PARRDR> Error: Repeated DIHE parameter ( 3163): CG2D CG2D CG2D HGA4 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3175): HGA4 CG2D CG2D HGA4 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3186): CG2D CG2D CG2D CG2D is replaced
PARRDR> Error: Repeated DIHE parameter ( 3187): CG2D CG2D CG2D CG2D is replaced
PARRDR> Error: Repeated DIHE parameter ( 3188): CG2D CG2D CG2D CG2D is replaced
PARRDR> Error: Repeated DIHE parameter ( 3186): CG2D CG2D CG2D CG2D is replaced
PARRDR> Error: Repeated DIHE parameter ( 3187): CG2D CG2D CG2D CG2D is replaced
PARRDR> Error: Repeated DIHE parameter ( 3188): CG2D CG2D CG2D CG2D is replaced
PARRDR> Error: Repeated DIHE parameter ( 3186): CG2D CG2D CG2D CG2D is replaced
PARRDR> Error: Repeated DIHE parameter ( 3187): CG2D CG2D CG2D CG2D is replaced
PARRDR> Error: Repeated DIHE parameter ( 3188): CG2D CG2D CG2D CG2D is replaced
PARRDR> Error: Repeated DIHE parameter ( 3192): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3193): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3194): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3195): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3196): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3192): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3193): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3194): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3195): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3196): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3192): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3193): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3194): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3195): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3196): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3192): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3193): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3194): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3195): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3196): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3192): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3193): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3194): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3195): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3196): CG2D CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3197): CG2D CG2D CG2D CG33 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3198): CG2D CG2D CG2D CG33 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3197): CG2D CG2D CG2D CG33 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3198): CG2D CG2D CG2D CG33 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3199): CG2D CG2D CG2D HGA4 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3244): HGA4 CG2D CG2D CG2D is replaced
PARRDR> Error: Repeated DIHE parameter ( 3246): HGA4 CG2D CG2D CG30 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3247): HGA4 CG2D CG2D CG33 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3249): HGA4 CG2D CG2D HGA4 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3331): CG2D CG2D CG2D CG2D is replaced
PARRDR> Error: Repeated DIHE parameter ( 3332): CG2D CG2D CG2D CG2D is replaced
PARRDR> Error: Repeated DIHE parameter ( 3331): CG2D CG2D CG2D CG2D is replaced
PARRDR> Error: Repeated DIHE parameter ( 3332): CG2D CG2D CG2D CG2D is replaced
PARRDR> Error: Repeated DIHE parameter ( 3339): CG2D CG2D CG2D CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3340): CG2D CG2D CG2D CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3339): CG2D CG2D CG2D CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3340): CG2D CG2D CG2D CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3341): CG2D CG2D CG2D CG33 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3342): CG2D CG2D CG2D CG33 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3341): CG2D CG2D CG2D CG33 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3342): CG2D CG2D CG2D CG33 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3343): CG2D CG2D CG2D HGA4 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3350): CG30 CG2D CG2D CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3351): CG30 CG2D CG2D CG33 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3352): CG32 CG2D CG2D CG33 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3354): CG33 CG2D CG2D HGA4 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3400): CG2D CG2D CG30 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3401): CG2D CG2D CG30 CG33 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3402): CG2D CG2D CG30 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3403): CG2D CG2D CG30 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3402): CG2D CG2D CG30 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3403): CG2D CG2D CG30 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3404): CG2D CG2D CG30 CG33 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3405): CG2D CG2D CG30 CG33 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3404): CG2D CG2D CG30 CG33 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3405): CG2D CG2D CG30 CG33 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3408): CG2D CG2D CG32 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3409): CG2D CG2D CG32 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3408): CG2D CG2D CG32 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3409): CG2D CG2D CG32 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3410): CG2D CG2D CG32 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3411): CG2D CG2D CG32 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3412): CG2D CG2D CG32 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3410): CG2D CG2D CG32 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3411): CG2D CG2D CG32 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3412): CG2D CG2D CG32 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3410): CG2D CG2D CG32 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3411): CG2D CG2D CG32 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3412): CG2D CG2D CG32 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3414): CG2D CG2D CG32 HGA2 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3417): CG33 CG2D CG32 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3418): CG33 CG2D CG32 HGA2 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3419): HGA4 CG2D CG32 OG31 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3421): HGA4 CG2D CG32 HGA2 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3422): CG2D CG2D CG33 HGA3 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3423): CG2D CG2D CG33 HGA3 is replaced
PARRDR> Error: Repeated DIHE parameter ( 3425): CG32 CG2D CG33 HGA3 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5143): CG2D CG30 CG32 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5144): CG2D CG30 CG32 HGA2 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5149): CG33 CG30 CG32 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5153): CG33 CG30 CG32 HGA2 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5158): CG2D CG30 CG33 HGA3 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5161): CG32 CG30 CG33 HGA3 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5162): CG33 CG30 CG33 HGA3 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5516): CG2D CG32 CG32 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5517): CG2D CG32 CG32 HGA2 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5558): CG30 CG32 CG32 CG32 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5559): CG30 CG32 CG32 HGA2 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5601): CG32 CG32 CG32 HGA2 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5641): HGA2 CG32 CG32 HGA2 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5937): CG2D CG32 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5938): CG2D CG32 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5939): CG2D CG32 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5937): CG2D CG32 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5938): CG2D CG32 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5939): CG2D CG32 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5937): CG2D CG32 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5938): CG2D CG32 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5939): CG2D CG32 OG31 HGP1 is replaced
PARRDR> Error: Repeated DIHE parameter ( 5965): HGA2 CG32 OG31 HGP1 is replaced
PARMIO> NONBOND, HBOND lists and IMAGE atoms cleared.


Kindly requesting someone to explain this since I am new to CHRAMM and Does it have a big impact on the complex.psf?Is there anyway to overcome this?

Thanks
VH

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#37680 - 10/29/19 12:06 PM Re: Repeated BOND parameter ( 482): CG2D CG2D is replaced [Re: vht]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8406
Loc: 39 03 48 N, 77 06 54 W
Difficult to say; it depends on the parameter values for both the original and replaced parameters. It's an indication that someone has been very sloppy about the contents of one or more parameter files.
_________________________
Rick Venable
computational chemist


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#37687 - 11/01/19 06:13 AM Re: Repeated BOND parameter ( 482): CG2D CG2D is replaced [Re: vht]
vht Offline
Forum Member

Registered: 10/24/19
Posts: 6
By considering this,

PARRDR> Error: Repeated BOND parameter ( 482): CG2D CG2D is replaced

According to the above, CG2D is replaced and but I am unable to find the .prm file in this case.

Do you have any idea in which file that it might be replaced?


Thanks


Edited by vht (11/01/19 06:20 AM)

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#37688 - 11/01/19 11:56 AM Re: Repeated BOND parameter ( 482): CG2D CG2D is replaced [Re: vht]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8406
Loc: 39 03 48 N, 77 06 54 W
The atom names have been truncated to four characters in the error messages, as there are still some cases where the code has (unfortunately) not been updated to support eight character atom names. You need to look for atom names which begin with CG2D and not an exact match. The original CGenFF parameter file has these atoms:

Code:
MASS  -1  CG2D1     12.01100 ! alkene; RHC= ; imine C
MASS  -1  CG2D2     12.01100 ! alkene; H2C=
MASS  -1  CG2D1O    12.01100 ! double bond C adjacent to heteroatom. In conjugated systems, the atom to which it is double bonded must be CG2DC1.
MASS  -1  CG2D2O    12.01100 ! double bond C adjacent to heteroatom. In conjugated systems, the atom to which it is double bonded must be CG2DC2.
MASS  -1  CG2DC1    12.01100 ! conjugated alkenes, R2C=CR2
MASS  -1  CG2DC2    12.01100 ! conjugated alkenes, R2C=CR2
MASS  -1  CG2DC3    12.01100 ! conjugated alkenes, H2C=
_________________________
Rick Venable
computational chemist


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