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#8406 - 10/02/05 08:45 AM "DOUBLE BOND SPECS FOR SOME ATOM PAIRS"
asykes Offline
Forum Member

Registered: 05/30/05
Posts: 77
Loc: Heswall, Wirral, England
I have created a new residue as shown below (GAMESS HF/6-31G*):

RESI SIX 0.00
ATOM O3 OE -0.794557
ATOM N NP -0.549737
ATOM CA CT 0.076491
ATOM C C 0.52412
ATOM O O -0.507999
ATOM C8 CT 0.189929
ATOM C9 CT -0.306091
ATOM C10 CT -0.335846
ATOM C11 CT 0.167235
ATOM C12 CT -0.087568
ATOM O22 OT -0.750312
ATOM H2 H 0.338434
ATOM H1 HA 0.227151
ATOM H4 HA 0.158833
ATOM H5 HA 0.204446
ATOM H6 HA 0.162848
ATOM H7 HA 0.182302
ATOM H8 HA 0.170315
ATOM H9 HA 0.174668
ATOM H11 HA 0.173927
ATOM H12 HA 0.168520
ATOM H10 H 0.412892
BOND N -C
BOND +N C
BOND CA C
BOND O3 CA
BOND C8 O3
BOND C O
BOND C8 C9
BOND C9 C10
BOND C10 C11
BOND CA C11
BOND C12 C8
BOND C12 N
BOND C11 O22
BOND N H2
BOND CA H1
BOND C8 H4
BOND C9 H5
BOND C9 H6
BOND C10 H7
BOND C10 H8
BOND C11 H9
BOND C12 H11
BOND C12 H12
BOND O22 H10
dihe H1 CA C O
dihe C11 CA C O
dihe O3 CA C O
dihe C8 O3 CA H1
dihe C8 O3 CA C11
dihe C8 O3 CA C
dihe H4 C8 O3 CA
dihe C12 C8 O3 CA
dihe C9 C8 O3 CA
dihe H4 C8 C9 H6
dihe H4 C8 C9 H5
dihe H4 C8 C9 C10
dihe C12 C8 C9 H6
dihe C12 C8 C9 H5
dihe C12 C8 C9 C10
dihe O3 C8 C9 H6
dihe O3 C8 C9 H5
dihe O3 C8 C9 C10
dihe H6 C9 C10 H8
dihe H6 C9 C10 H7
dihe H6 C9 C10 C11
dihe H5 C9 C10 H8
dihe H5 C9 C10 H7
dihe H5 C9 C10 C11
dihe C8 C9 C10 H8
dihe C8 C9 C10 H7
dihe C8 C9 C10 C11
dihe H8 C10 C11 H9
dihe H8 C10 C11 O22
dihe H8 C10 C11 CA
dihe H7 C10 C11 H9
dihe H7 C10 C11 O22
dihe H7 C10 C11 CA
dihe C9 C10 C11 H9
dihe C9 C10 C11 O22
dihe C9 C10 C11 CA
dihe H1 CA C11 H9
dihe H1 CA C11 O22
dihe H1 CA C11 C10
dihe O3 CA C11 H9
dihe O3 CA C11 O22
dihe O3 CA C11 C10
dihe C CA C11 H9
dihe C CA C11 O22
dihe C CA C11 C10
dihe H12 C12 C8 H4
dihe H12 C12 C8 C9
dihe H12 C12 C8 O3
dihe H11 C12 C8 H4
dihe H11 C12 C8 C9
dihe H11 C12 C8 O3
dihe N C12 C8 H4
dihe N C12 C8 C9
dihe N C12 C8 O3
dihe H12 C12 N H2
dihe H11 C12 N H2
dihe C8 C12 N H2
dihe H9 C11 O22 H10
dihe CA C11 O22 H10
dihe C10 C11 O22 H10

However, when I GENErate it within a script I get the error message, "DOUBLE BOND SPECS FOR SOME ATOM PAIRS".
I have searched the forums and found that this relates to a bond being defined more than once, but the bonds are defined only once each. Is there anything else that could be causing this error?

Thanks


Edited by asykes (10/02/05 11:17 AM)
_________________________
Adam Sykes ----------- The University of Liverpool Liverpool, UK ----------- e: adam.sykes@liv.ac.uk

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#8407 - 10/02/05 02:24 PM Re: "DOUBLE BOND SPECS FOR SOME ATOM PAIRS" [Re: asykes]
lennart Online   content

Forum Member

Registered: 09/25/03
Posts: 4742
Loc: ~ 59N, 15E
No, you have overspecified your bond list - check again! /hint: what happens when you have more than one residue in a chain?/

You should probably let CHARMM generate your dihedrals, ie remove the dihe... statements.
_________________________
Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden

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#8408 - 10/02/05 07:58 PM Re: "DOUBLE BOND SPECS FOR SOME ATOM PAIRS" [Re: asykes]
asykes Offline
Forum Member

Registered: 05/30/05
Posts: 77
Loc: Heswall, Wirral, England
I have now got the following, still no luck. I am sure I missing something very simple but can't see it.

RESI SIX 0.00
ATOM O3 OE -0.794557
ATOM N NP -0.549737
ATOM CA CT 0.076491
ATOM C C 0.52412
ATOM O O -0.507999
ATOM C8 CT 0.189929
ATOM C9 CT -0.306091
ATOM C10 CT -0.335846
ATOM C11 CT 0.167235
ATOM C12 CT -0.087568
ATOM O22 OT -0.750312
ATOM H2 H 0.338434
ATOM H1 HA 0.227151
ATOM H4 HA 0.158833
ATOM H5 HA 0.204446
ATOM H6 HA 0.162848
ATOM H7 HA 0.182302
ATOM H8 HA 0.170315
ATOM H9 HA 0.174668
ATOM H11 HA 0.173927
ATOM H12 HA 0.168520
ATOM H10 H 0.412892
BOND CA H1 CA C CA O3 CA C11
BOND O3 C8
BOND C8 H4 C8 C9 C8 C12
BOND C9 H5 C9 C10
BOND C10 H8 C10 H7 C10 C11
BOND C11 H9 C11 O22
BOND C CA
BOND C12 H12 C12 H11 C12 N
BOND N H2
DOUBLE C O
BOND C +N

Thanks for your help.
_________________________
Adam Sykes ----------- The University of Liverpool Liverpool, UK ----------- e: adam.sykes@liv.ac.uk

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#8409 - 10/03/05 12:57 PM Re: "DOUBLE BOND SPECS FOR SOME ATOM PAIRS" [Re: asykes]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8379
Loc: 39 03 48 N, 77 06 54 W
BOND CA H1 CA C CA O3 CA C11
BOND O3 C8
BOND C8 H4 C8 C9 C8 C12
BOND C9 H5 C9 C10
BOND C10 H8 C10 H7 C10 C11
BOND C11 H9 C11 O22
BOND C CA
BOND C12 H12 C12 H11 C12 N
BOND N H2
DOUBLE C O
BOND C +N
_________________________
Rick Venable
computational chemist


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#8410 - 10/03/05 07:01 PM Re: "DOUBLE BOND SPECS FOR SOME ATOM PAIRS" [Re: rmv]
asykes Offline
Forum Member

Registered: 05/30/05
Posts: 77
Loc: Heswall, Wirral, England
Thanks for the help. I couldn't see for looking. That part works fine now.
_________________________
Adam Sykes ----------- The University of Liverpool Liverpool, UK ----------- e: adam.sykes@liv.ac.uk

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