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Repeated BOND parameter ( 482): CG2D CG2D is replaced
#37678 10/29/19 08:31 AM
Joined: Oct 2019
Posts: 17
V
vht Online Content OP
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vht
Forum Member
V
Joined: Oct 2019
Posts: 17
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
Re: Repeated BOND parameter ( 482): CG2D CG2D is replaced
vht #37680 10/29/19 04:06 PM
Joined: Sep 2003
Posts: 8,479
39 03 48 N, 77 06 54 W
rmv Online Content
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rmv
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Joined: Sep 2003
Posts: 8,479
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
Re: Repeated BOND parameter ( 482): CG2D CG2D is replaced
vht #37687 11/01/19 10:13 AM
Joined: Oct 2019
Posts: 17
V
vht Online Content OP
Forum Member
OP Online Content
vht
Forum Member
V
Joined: Oct 2019
Posts: 17
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

Last edited by vht; 11/01/19 10:20 AM.
Re: Repeated BOND parameter ( 482): CG2D CG2D is replaced
vht #37688 11/01/19 03:56 PM
Joined: Sep 2003
Posts: 8,479
39 03 48 N, 77 06 54 W
rmv Online Content
Forum Member
Online Content
rmv
Forum Member
Joined: Sep 2003
Posts: 8,479
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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