# Re: [AMBER] problem converting AmbertoDesmond

From: Albert <mailmd2011.gmail.com>
Date: Tue, 17 Apr 2012 08:03:43 +0200

On 04/16/2012 09:30 PM, David A Case wrote:
> All I can say here is that, according to what I have been told(!?!), this step
> is not needed. I'm guessing that atoms 4683 to 4685 form a water molecule,
> and Amber typically does not keep the force constants for those. Given LEaP
> the command "set default flexible water on" before making the Amber prmtop
> may help.
>
> ....dac

hello:
when I turn the "set default flexible water on" and write the toplogy
and paramter files, it said:

1-4: angle 36275 36276 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36278 36279 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36281 36282 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36284 36285 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36287 36288 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36290 36291 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36293 36294 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36296 36297 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36299 36300 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36302 36303 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36305 36306 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36308 36309 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36311 36312 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36314 36315 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36317 36318 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36320 36321 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36323 36324 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36326 36327 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36329 36330 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36332 36333 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36335 36336 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36338 36339 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36341 36342 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36344 36345 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36347 36348 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36350 36351 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36353 36354 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36356 36357 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36359 36360 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36362 36363 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36365 36366 duplicates bond ('triangular' bond) or angle
('square' bond)

1-4: angle 36368 36369 duplicates bond ('triangular' bond) or angle
('square' bond)

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Received on Mon Apr 16 2012 - 23:30:04 PDT
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