Hi,
After creating all the essential files, when I attempted to run tleap for
creation of prmtop & inpcrd files with the attached script I am getting the
following errors:
WARNING: There is a bond of 7.153070 angstroms between:
------- .R<DA 308>.A<C6 18> and .R<DA 308>.A<N1 22>
WARNING: There is a bond of 7.664037 angstroms between:
------- .R<DA 308>.A<C5 17> and .R<DA 308>.A<C4 26>
WARNING: There is a bond of 8.325558 angstroms between:
------- .R<DA 308>.A<C8 14> and .R<DA 308>.A<N7 16>
WARNING: There is a bond of 9.177835 angstroms between:
------- .R<DA3 309>.A<C6 18> and .R<DA3 309>.A<N1 22>
WARNING: There is a bond of 9.046964 angstroms between:
------- .R<DA3 309>.A<C5 17> and .R<DA3 309>.A<C4 26>
WARNING: There is a bond of 10.643195 angstroms between:
------- .R<DA3 309>.A<C8 14> and .R<DA3 309>.A<N7 16>
WARNING: There is a bond of 5.466846 angstroms between:
------- .R<DA3 314>.A<C6 18> and .R<DA3 314>.A<N1 22>
WARNING: There is a bond of 5.951165 angstroms between:
------- .R<DA3 314>.A<C5 17> and .R<DA3 314>.A<C4 26>
WARNING: There is a bond of 6.594169 angstroms between:
------- .R<DA3 314>.A<C8 14> and .R<DA3 314>.A<N7 16>
WARNING: There is a bond of 17.898839 angstroms between:
------- .R<DA 316>.A<C2 23> and .R<DA 316>.A<N3 25>
WARNING: There is a bond of 18.767763 angstroms between:
------- .R<DA 316>.A<C6 18> and .R<DA 316>.A<N1 22>
WARNING: There is a bond of 17.088990 angstroms between:
------- .R<DA3 317>.A<C2 23> and .R<DA3 317>.A<N3 25>
WARNING: There is a bond of 17.843489 angstroms between:
------- .R<DA3 317>.A<C6 18> and .R<DA3 317>.A<N1 22>
WARNING: There is a bond of 18.561922 angstroms between:
------- .R<DA3 322>.A<C2 23> and .R<DA3 322>.A<N3 25>
WARNING: There is a bond of 18.885253 angstroms between:
------- .R<DA3 322>.A<C6 18> and .R<DA3 322>.A<N1 22>
WARNING: There is a bond of 13.642547 angstroms between:
------- .R<DT3 324>.A<C2 25> and .R<DT3 324>.A<O2 26>
WARNING: There is a bond of 3.511072 angstroms between:
------- .R<DT3 324>.A<C5 16> and .R<DT3 324>.A<C4 21>
WARNING: There is a bond of 9.228533 angstroms between:
------- .R<DT3 326>.A<C2 25> and .R<DT3 326>.A<O2 26>
WARNING: There is a bond of 3.475075 angstroms between:
------- .R<DT3 326>.A<C5 16> and .R<DT3 326>.A<C4 21>
WARNING: There is a bond of 13.086906 angstroms between:
------- .R<DT3 328>.A<C2 25> and .R<DT3 328>.A<O2 26>
WARNING: There is a bond of 3.509011 angstroms between:
------- .R<DT3 328>.A<C5 16> and .R<DT3 328>.A<C4 21>
WARNING: There is a bond of 12.807218 angstroms between:
------- .R<DT3 331>.A<N3 23> and .R<DT3 331>.A<C2 25>
WARNING: There is a bond of 11.273166 angstroms between:
------- .R<DT3 331>.A<C5 16> and .R<DT3 331>.A<C4 21>
WARNING: There is a bond of 18.614223 angstroms between:
------- .R<DT3 333>.A<N3 23> and .R<DT3 333>.A<C2 25>
WARNING: There is a bond of 17.368405 angstroms between:
------- .R<DT3 333>.A<C5 16> and .R<DT3 333>.A<C4 21>
WARNING: There is a bond of 19.006298 angstroms between:
------- .R<DT3 335>.A<N3 23> and .R<DT3 335>.A<C2 25>
WARNING: There is a bond of 17.352783 angstroms between:
------- .R<DT3 335>.A<C5 16> and .R<DT3 335>.A<C4 21>
WARNING: There is a bond of 12.671686 angstroms between:
------- .R<DG 337>.A<C6 18> and .R<DG 337>.A<O6 19>
WARNING: There is a bond of 9.413222 angstroms between:
------- .R<DG3 338>.A<C6 18> and .R<DG3 338>.A<O6 19>
WARNING: There is a bond of 12.279124 angstroms between:
------- .R<DG 340>.A<C6 18> and .R<DG 340>.A<O6 19>
WARNING: There is a bond of 8.850682 angstroms between:
------- .R<DG3 341>.A<C6 18> and .R<DG3 341>.A<O6 19>
WARNING: There is a bond of 18.722110 angstroms between:
------- .R<DG 343>.A<C6 18> and .R<DG 343>.A<O6 19>
WARNING: There is a bond of 16.935773 angstroms between:
------- .R<DG3 344>.A<C6 18> and .R<DG3 344>.A<O6 19>
WARNING: There is a bond of 12.855588 angstroms between:
------- .R<DG 346>.A<C6 18> and .R<DG 346>.A<O6 19>
WARNING: There is a bond of 10.722128 angstroms between:
------- .R<DG3 347>.A<C6 18> and .R<DG3 347>.A<O6 19>
WARNING: There is a bond of 14.510363 angstroms between:
------- .R<DT3 349>.A<C4 21> and .R<DT3 349>.A<O4 22>
WARNING: There is a bond of 17.796329 angstroms between:
------- .R<DT3 351>.A<C4 21> and .R<DT3 351>.A<O4 22>
WARNING: There is a bond of 20.612802 angstroms between:
------- .R<DT3 353>.A<C4 21> and .R<DT3 353>.A<O4 22>
WARNING: There is a bond of 11.507267 angstroms between:
------- .R<DT3 355>.A<N3 23> and .R<DT3 355>.A<C2 25>
WARNING: There is a bond of 11.094065 angstroms between:
------- .R<DT3 355>.A<C5 16> and .R<DT3 355>.A<C4 21>
WARNING: There is a bond of 18.662840 angstroms between:
------- .R<DT3 357>.A<N3 23> and .R<DT3 357>.A<C2 25>
WARNING: There is a bond of 17.834962 angstroms between:
------- .R<DT3 357>.A<C5 16> and .R<DT3 357>.A<C4 21>
WARNING: There is a bond of 16.858360 angstroms between:
------- .R<DT3 359>.A<N3 23> and .R<DT3 359>.A<C2 25>
WARNING: There is a bond of 16.139838 angstroms between:
------- .R<DT3 359>.A<C5 16> and .R<DT3 359>.A<C4 21>
WARNING: There is a bond of 11.387475 angstroms between:
------- .R<DA5 360>.A<O3' 30> and .R<DA 361>.A<P 1>
WARNING: There is a bond of 12.003352 angstroms between:
------- .R<DA 361>.A<O3' 32> and .R<DA 362>.A<P 1>
WARNING: There is a bond of 11.578537 angstroms between:
------- .R<DA 362>.A<O3' 32> and .R<DG 363>.A<P 1>
WARNING: There is a bond of 11.339985 angstroms between:
------- .R<DG 363>.A<O3' 33> and .R<DG 364>.A<P 1>
WARNING: There is a bond of 9.521937 angstroms between:
------- .R<DG 364>.A<O3' 33> and .R<DG 365>.A<P 1>
WARNING: There is a bond of 6.594453 angstroms between:
------- .R<DG 365>.A<O3' 33> and .R<DT 366>.A<P 1>
WARNING: There is a bond of 4.088225 angstroms between:
------- .R<DT 366>.A<O3' 32> and .R<DT 367>.A<P 1>
WARNING: There is a bond of 6.896254 angstroms between:
------- .R<DT 366>.A<C1' 11> and .R<DT 366>.A<N1 13>
WARNING: There is a bond of 5.293878 angstroms between:
------- .R<DT 367>.A<O3' 32> and .R<DA 368>.A<P 1>
WARNING: There is a bond of 6.609568 angstroms between:
------- .R<DT 367>.A<C1' 11> and .R<DT 367>.A<N1 13>
WARNING: There is a bond of 10.378578 angstroms between:
------- .R<DA 368>.A<O3' 32> and .R<DG 369>.A<P 1>
WARNING: There is a bond of 8.436336 angstroms between:
------- .R<DG 369>.A<O3' 33> and .R<DG 370>.A<P 1>
WARNING: There is a bond of 7.623567 angstroms between:
------- .R<DG 370>.A<O3' 33> and .R<DG 371>.A<P 1>
WARNING: There is a bond of 9.573801 angstroms between:
------- .R<DG 371>.A<O3' 33> and .R<DT 372>.A<P 1>
WARNING: There is a bond of 8.375198 angstroms between:
------- .R<DT 372>.A<O3' 32> and .R<DT 373>.A<P 1>
WARNING: There is a bond of 6.633651 angstroms between:
------- .R<DT 372>.A<C1' 11> and .R<DT 372>.A<N1 13>
WARNING: There is a bond of 8.228827 angstroms between:
------- .R<DT 373>.A<O3' 32> and .R<DA 374>.A<P 1>
WARNING: There is a bond of 7.022793 angstroms between:
------- .R<DT 373>.A<C1' 11> and .R<DT 373>.A<N1 13>
WARNING: There is a bond of 4.820366 angstroms between:
------- .R<DG 375>.A<O3' 33> and .R<DG 376>.A<P 1>
WARNING: There is a bond of 7.000659 angstroms between:
------- .R<DG 376>.A<O3' 33> and .R<DG 377>.A<P 1>
WARNING: There is a bond of 6.602596 angstroms between:
------- .R<DG 377>.A<O3' 33> and .R<DT 378>.A<P 1>
WARNING: There is a bond of 5.976624 angstroms between:
------- .R<DT 378>.A<O3' 32> and .R<DT 379>.A<P 1>
WARNING: There is a bond of 3.174098 angstroms between:
------- .R<DT 378>.A<C1' 11> and .R<DT 378>.A<N1 13>
WARNING: There is a bond of 9.477565 angstroms between:
------- .R<DT 379>.A<O3' 32> and .R<DA 380>.A<P 1>
WARNING: There is a bond of 6.544321 angstroms between:
------- .R<DT 379>.A<C1' 11> and .R<DT 379>.A<N1 13>
WARNING: There is a bond of 10.547713 angstroms between:
------- .R<DA 380>.A<O3' 32> and .R<DG 381>.A<P 1>
WARNING: There is a bond of 11.899850 angstroms between:
------- .R<DG 381>.A<O3' 33> and .R<DG 382>.A<P 1>
WARNING: There is a bond of 11.353009 angstroms between:
------- .R<DG 382>.A<O3' 33> and .R<DG 383>.A<P 1>
WARNING: There is a bond of 10.719439 angstroms between:
------- .R<DG 383>.A<O3' 33> and .R<DA3 384>.A<P 1>
WARNING: There is a bond of 9.566737 angstroms between:
------- .R<DA 386>.A<P 1> and .R<DA 386>.A<O5' 4>
WARNING: There is a bond of 7.439266 angstroms between:
------- .R<DG 389>.A<P 1> and .R<DG 389>.A<O5' 4>
WARNING: There is a bond of 6.529255 angstroms between:
------- .R<DA 392>.A<P 1> and .R<DA 392>.A<O5' 4>
WARNING: There is a bond of 10.421239 angstroms between:
------- .R<DG 393>.A<P 1> and .R<DG 393>.A<O5' 4>
WARNING: There is a bond of 4.928248 angstroms between:
------- .R<DG 395>.A<P 1> and .R<DG 395>.A<O5' 4>
WARNING: There is a bond of 7.037775 angstroms between:
------- .R<DT 396>.A<P 1> and .R<DT 396>.A<O5' 4>
WARNING: There is a bond of 7.916284 angstroms between:
------- .R<DT 397>.A<P 1> and .R<DT 397>.A<O5' 4>
WARNING: There is a bond of 4.346331 angstroms between:
------- .R<DA 398>.A<P 1> and .R<DA 398>.A<O5' 4>
WARNING: There is a bond of 6.953484 angstroms between:
------- .R<DG 399>.A<P 1> and .R<DG 399>.A<O5' 4>
WARNING: There is a bond of 4.782456 angstroms between:
------- .R<DG 400>.A<P 1> and .R<DG 400>.A<O5' 4>
WARNING: There is a bond of 3.771135 angstroms between:
------- .R<DG 401>.A<P 1> and .R<DG 401>.A<O5' 4>
WARNING: There is a bond of 9.422124 angstroms between:
------- .R<DT 403>.A<P 1> and .R<DT 403>.A<O5' 4>
WARNING: There is a bond of 6.926406 angstroms between:
------- .R<DA 404>.A<P 1> and .R<DA 404>.A<O5' 4>
WARNING: There is a bond of 5.274296 angstroms between:
------- .R<DG 405>.A<P 1> and .R<DG 405>.A<O5' 4>
WARNING: There is a bond of 3.177268 angstroms between:
------- .R<DG 406>.A<P 1> and .R<DG 406>.A<O5' 4>
WARNING: There is a bond of 6.767584 angstroms between:
------- .R<DG 407>.A<P 1> and .R<DG 407>.A<O5' 4>
WARNING: There is a bond of 4.633268 angstroms between:
------- .R<DA 408>.A<P 1> and .R<DA 408>.A<O5' 4>
WARNING: There is a bond of 9.579224 angstroms between:
------- .R<DG 411>.A<C6 18> and .R<DG 411>.A<N1 20>
WARNING: There is a bond of 11.870696 angstroms between:
------- .R<DG 411>.A<C5 17> and .R<DG 411>.A<C6 18>
WARNING: There is a bond of 3.537058 angstroms between:
------- .R<DG3 412>.A<C6 18> and .R<DG3 412>.A<N1 20>
WARNING: There is a bond of 5.772166 angstroms between:
------- .R<DG3 412>.A<C5 17> and .R<DG3 412>.A<C6 18>
WARNING: There is a bond of 11.021893 angstroms between:
------- .R<DG 414>.A<C6 18> and .R<DG 414>.A<N1 20>
WARNING: There is a bond of 13.276592 angstroms between:
------- .R<DG 414>.A<C5 17> and .R<DG 414>.A<C6 18>
WARNING: There is a bond of 5.038627 angstroms between:
------- .R<DG3 415>.A<C6 18> and .R<DG3 415>.A<N1 20>
WARNING: There is a bond of 7.310607 angstroms between:
------- .R<DG3 415>.A<C5 17> and .R<DG3 415>.A<C6 18>
WARNING: There is a bond of 13.891206 angstroms between:
------- .R<DG 417>.A<C6 18> and .R<DG 417>.A<N1 20>
WARNING: There is a bond of 16.193777 angstroms between:
------- .R<DG 417>.A<C5 17> and .R<DG 417>.A<C6 18>
WARNING: There is a bond of 15.647765 angstroms between:
------- .R<DG3 418>.A<C6 18> and .R<DG3 418>.A<N1 20>
WARNING: There is a bond of 17.538990 angstroms between:
------- .R<DG3 418>.A<C5 17> and .R<DG3 418>.A<C6 18>
WARNING: There is a bond of 8.879565 angstroms between:
------- .R<DG 420>.A<C6 18> and .R<DG 420>.A<N1 20>
WARNING: There is a bond of 11.190274 angstroms between:
------- .R<DG 420>.A<C5 17> and .R<DG 420>.A<C6 18>
WARNING: There is a bond of 5.799604 angstroms between:
------- .R<DG3 421>.A<C6 18> and .R<DG3 421>.A<N1 20>
WARNING: There is a bond of 8.128926 angstroms between:
------- .R<DG3 421>.A<C5 17> and .R<DG3 421>.A<C6 18>
WARNING: There is a bond of 7.357587 angstroms between:
------- .R<DA5 422>.A<O3' 30> and .R<DA 423>.A<P 1>
WARNING: There is a bond of 6.385946 angstroms between:
------- .R<DA 423>.A<O3' 32> and .R<DA 424>.A<P 1>
WARNING: There is a bond of 3.805169 angstroms between:
------- .R<DA 424>.A<O3' 32> and .R<DG 425>.A<P 1>
WARNING: There is a bond of 5.132259 angstroms between:
------- .R<DG 425>.A<O3' 33> and .R<DG 426>.A<P 1>
WARNING: There is a bond of 3.980577 angstroms between:
------- .R<DG 426>.A<O3' 33> and .R<DG3 427>.A<P 1>
WARNING: There is a bond of 10.068160 angstroms between:
------- .R<DA5 428>.A<O3' 30> and .R<DG 429>.A<P 1>
WARNING: There is a bond of 7.233288 angstroms between:
------- .R<DG 429>.A<O3' 33> and .R<DG 430>.A<P 1>
WARNING: There is a bond of 8.021535 angstroms between:
------- .R<DG 430>.A<O3' 33> and .R<DG3 431>.A<P 1>
WARNING: There is a bond of 11.592017 angstroms between:
------- .R<DA5 432>.A<O3' 30> and .R<DG 433>.A<P 1>
WARNING: There is a bond of 6.935345 angstroms between:
------- .R<DG 433>.A<O3' 33> and .R<DG 434>.A<P 1>
WARNING: There is a bond of 6.068556 angstroms between:
------- .R<DG 434>.A<O3' 33> and .R<DG3 435>.A<P 1>
WARNING: There is a bond of 9.796204 angstroms between:
------- .R<DA5 436>.A<O3' 30> and .R<DG 437>.A<P 1>
WARNING: There is a bond of 5.132133 angstroms between:
------- .R<DG 437>.A<O3' 33> and .R<DG 438>.A<P 1>
WARNING: There is a bond of 3.560939 angstroms between:
------- .R<DG 438>.A<O3' 33> and .R<DG 439>.A<P 1>
WARNING: There is a bond of 4.417449 angstroms between:
------- .R<DG 439>.A<O3' 33> and .R<DA 440>.A<P 1>
WARNING: There is a bond of 5.360113 angstroms between:
------- .R<DA 440>.A<O3' 32> and .R<DA3 441>.A<P 1>
WARNING: There is a bond of 7.053996 angstroms between:
------- .R<DT5 442>.A<O3' 30> and .R<DT3 443>.A<P 1>
WARNING: There is a bond of 13.313147 angstroms between:
------- .R<DT5 444>.A<O3' 30> and .R<DT3 445>.A<P 1>
WARNING: There is a bond of 13.175595 angstroms between:
------- .R<DT5 446>.A<O3' 30> and .R<DT3 447>.A<P 1>
WARNING: There is a bond of 11.759594 angstroms between:
------- .R<DA5 449>.A<O3' 30> and .R<DA 450>.A<P 1>
WARNING: There is a bond of 9.109937 angstroms between:
------- .R<DA 450>.A<O3' 32> and .R<DA 451>.A<P 1>
WARNING: There is a bond of 9.064384 angstroms between:
------- .R<DA 451>.A<O3' 32> and .R<DG 452>.A<P 1>
WARNING: There is a bond of 6.143249 angstroms between:
------- .R<DG 452>.A<O3' 33> and .R<DG 453>.A<P 1>
WARNING: There is a bond of 4.111433 angstroms between:
------- .R<DG 453>.A<O3' 33> and .R<DG 454>.A<P 1>
WARNING: There is a bond of 9.106094 angstroms between:
------- .R<DG 454>.A<O3' 33> and .R<DT 455>.A<P 1>
WARNING: There is a bond of 8.871541 angstroms between:
------- .R<DT 455>.A<O3' 32> and .R<DT 456>.A<P 1>
WARNING: There is a bond of 5.568623 angstroms between:
------- .R<DT 456>.A<O3' 32> and .R<DA 457>.A<P 1>
WARNING: There is a bond of 4.798087 angstroms between:
------- .R<DA 457>.A<O3' 32> and .R<DG 458>.A<P 1>
WARNING: There is a bond of 4.577403 angstroms between:
------- .R<DG 458>.A<O3' 33> and .R<DG 459>.A<P 1>
WARNING: There is a bond of 5.957431 angstroms between:
------- .R<DG 459>.A<O3' 33> and .R<DG 460>.A<P 1>
WARNING: There is a bond of 6.940902 angstroms between:
------- .R<DG 460>.A<O3' 33> and .R<DT 461>.A<P 1>
WARNING: There is a bond of 10.699647 angstroms between:
------- .R<DT 461>.A<O3' 32> and .R<DT 462>.A<P 1>
WARNING: There is a bond of 10.082699 angstroms between:
------- .R<DT 462>.A<O3' 32> and .R<DA 463>.A<P 1>
WARNING: There is a bond of 7.117849 angstroms between:
------- .R<DA 463>.A<O3' 32> and .R<DG 464>.A<P 1>
WARNING: There is a bond of 4.466391 angstroms between:
------- .R<DG 464>.A<O3' 33> and .R<DG 465>.A<P 1>
WARNING: There is a bond of 5.787017 angstroms between:
------- .R<DG 465>.A<O3' 33> and .R<DG 466>.A<P 1>
WARNING: There is a bond of 8.381399 angstroms between:
------- .R<DG 466>.A<O3' 33> and .R<DT 467>.A<P 1>
WARNING: There is a bond of 12.853988 angstroms between:
------- .R<DT 467>.A<O3' 32> and .R<DT 468>.A<P 1>
WARNING: There is a bond of 8.683917 angstroms between:
------- .R<DT 468>.A<O3' 32> and .R<DA 469>.A<P 1>
WARNING: There is a bond of 11.220713 angstroms between:
------- .R<DA 469>.A<O3' 32> and .R<DG 470>.A<P 1>
WARNING: There is a bond of 8.396954 angstroms between:
------- .R<DG 470>.A<O3' 33> and .R<DG 471>.A<P 1>
WARNING: There is a bond of 8.711844 angstroms between:
------- .R<DG 471>.A<O3' 33> and .R<DG 472>.A<P 1>
WARNING: There is a bond of 8.624905 angstroms between:
------- .R<DG 472>.A<O3' 33> and .R<DA 473>.A<P 1>
WARNING: There is a bond of 5.748261 angstroms between:
------- .R<DA 473>.A<O3' 32> and .R<DA3 474>.A<P 1>
WARNING: There is a bond of 14.363358 angstroms between:
------- .R<DA 477>.A<C6 18> and .R<DA 477>.A<N6 19>
WARNING: There is a bond of 14.146962 angstroms between:
------- .R<DA3 478>.A<C6 18> and .R<DA3 478>.A<N6 19>
WARNING: There is a bond of 7.466201 angstroms between:
------- .R<DA5 482>.A<O3' 30> and .R<DA3 483>.A<P 1>
WARNING: There is a bond of 14.789645 angstroms between:
------- .R<DA3 483>.A<C6 18> and .R<DA3 483>.A<N6 19>
WARNING: There is a bond of 7.078283 angstroms between:
------- .R<DA5 484>.A<O3' 30> and .R<DA 485>.A<P 1>
WARNING: There is a bond of 8.947204 angstroms between:
------- .R<DA 485>.A<O3' 32> and .R<DA 486>.A<P 1>
WARNING: There is a bond of 9.765315 angstroms between:
------- .R<DA 486>.A<O3' 32> and .R<DG 487>.A<P 1>
WARNING: There is a bond of 9.032033 angstroms between:
------- .R<DG 487>.A<O3' 33> and .R<DG 488>.A<P 1>
WARNING: There is a bond of 5.573306 angstroms between:
------- .R<DG 488>.A<O3' 33> and .R<DG 489>.A<P 1>
WARNING: There is a bond of 9.103239 angstroms between:
------- .R<DG 489>.A<O3' 33> and .R<DT 490>.A<P 1>
WARNING: There is a bond of 11.431863 angstroms between:
------- .R<DT 490>.A<O3' 32> and .R<DT 491>.A<P 1>
WARNING: There is a bond of 9.503382 angstroms between:
------- .R<DA 492>.A<O3' 32> and .R<DG 493>.A<P 1>
WARNING: There is a bond of 7.697946 angstroms between:
------- .R<DG 493>.A<O3' 33> and .R<DG 494>.A<P 1>
WARNING: There is a bond of 9.461391 angstroms between:
------- .R<DG 494>.A<O3' 33> and .R<DG 495>.A<P 1>
WARNING: There is a bond of 6.848442 angstroms between:
------- .R<DG 495>.A<O3' 33> and .R<DT 496>.A<P 1>
WARNING: There is a bond of 7.398318 angstroms between:
------- .R<DT 496>.A<O3' 32> and .R<DT 497>.A<P 1>
WARNING: There is a bond of 10.053949 angstroms between:
------- .R<DT 497>.A<O3' 32> and .R<DA 498>.A<P 1>
WARNING: There is a bond of 7.438765 angstroms between:
------- .R<DA 498>.A<O3' 32> and .R<DG 499>.A<P 1>
WARNING: There is a bond of 11.896236 angstroms between:
------- .R<DG 500>.A<O3' 33> and .R<DG 501>.A<P 1>
WARNING: There is a bond of 6.410007 angstroms between:
------- .R<DG 501>.A<O3' 33> and .R<DT 502>.A<P 1>
WARNING: There is a bond of 8.896186 angstroms between:
------- .R<DT 502>.A<O3' 32> and .R<DT 503>.A<P 1>
WARNING: There is a bond of 7.911653 angstroms between:
------- .R<DT 503>.A<O3' 32> and .R<DA 504>.A<P 1>
WARNING: There is a bond of 11.031427 angstroms between:
------- .R<DA 504>.A<O3' 32> and .R<DG 505>.A<P 1>
WARNING: There is a bond of 9.460802 angstroms between:
------- .R<DG 505>.A<O3' 33> and .R<DG 506>.A<P 1>
WARNING: There is a bond of 7.112801 angstroms between:
------- .R<DG 506>.A<O3' 33> and .R<DG 507>.A<P 1>
WARNING: There is a bond of 11.915005 angstroms between:
------- .R<DG 507>.A<O3' 33> and .R<DA 508>.A<P 1>
WARNING: There is a bond of 7.380356 angstroms between:
------- .R<DA 508>.A<O3' 32> and .R<DA3 509>.A<P 1>
WARNING: There is a bond of 12.120535 angstroms between:
------- .R<DA 511>.A<P 1> and .R<DA 511>.A<O1P 2>
WARNING: There is a bond of 11.790494 angstroms between:
------- .R<DA 511>.A<P 1> and .R<DA 511>.A<O2P 3>
WARNING: There is a bond of 4.206482 angstroms between:
------- .R<DG 512>.A<P 1> and .R<DG 512>.A<O1P 2>
WARNING: There is a bond of 11.542484 angstroms between:
------- .R<DG 513>.A<P 1> and .R<DG 513>.A<O1P 2>
WARNING: There is a bond of 9.762871 angstroms between:
------- .R<DG 513>.A<P 1> and .R<DG 513>.A<O2P 3>
WARNING: There is a bond of 13.428734 angstroms between:
------- .R<DG 514>.A<P 1> and .R<DG 514>.A<O1P 2>
WARNING: There is a bond of 12.901358 angstroms between:
------- .R<DG 514>.A<P 1> and .R<DG 514>.A<O2P 3>
WARNING: There is a bond of 10.441249 angstroms between:
------- .R<DT 515>.A<P 1> and .R<DT 515>.A<O1P 2>
WARNING: There is a bond of 12.653080 angstroms between:
------- .R<DT 515>.A<P 1> and .R<DT 515>.A<O2P 3>
WARNING: There is a bond of 15.637736 angstroms between:
------- .R<DT 516>.A<P 1> and .R<DT 516>.A<O1P 2>
WARNING: There is a bond of 14.730868 angstroms between:
------- .R<DT 516>.A<P 1> and .R<DT 516>.A<O2P 3>
WARNING: There is a bond of 9.253538 angstroms between:
------- .R<DA 517>.A<P 1> and .R<DA 517>.A<O1P 2>
WARNING: There is a bond of 11.195561 angstroms between:
------- .R<DA 517>.A<P 1> and .R<DA 517>.A<O2P 3>
WARNING: There is a bond of 19.690485 angstroms between:
------- .R<DG 518>.A<P 1> and .R<DG 518>.A<O1P 2>
WARNING: There is a bond of 17.225673 angstroms between:
------- .R<DG 518>.A<P 1> and .R<DG 518>.A<O2P 3>
WARNING: There is a bond of 18.990189 angstroms between:
------- .R<DG 519>.A<P 1> and .R<DG 519>.A<O1P 2>
WARNING: There is a bond of 19.783130 angstroms between:
------- .R<DG 519>.A<P 1> and .R<DG 519>.A<O2P 3>
WARNING: There is a bond of 18.593060 angstroms between:
------- .R<DG 520>.A<P 1> and .R<DG 520>.A<O1P 2>
WARNING: There is a bond of 19.392658 angstroms between:
------- .R<DG 520>.A<P 1> and .R<DG 520>.A<O2P 3>
WARNING: There is a bond of 24.521129 angstroms between:
------- .R<DT 521>.A<P 1> and .R<DT 521>.A<O1P 2>
WARNING: There is a bond of 22.584252 angstroms between:
------- .R<DT 521>.A<P 1> and .R<DT 521>.A<O2P 3>
WARNING: There is a bond of 16.706764 angstroms between:
------- .R<DT 522>.A<P 1> and .R<DT 522>.A<O1P 2>
WARNING: There is a bond of 18.441172 angstroms between:
------- .R<DT 522>.A<P 1> and .R<DT 522>.A<O2P 3>
WARNING: There is a bond of 21.882168 angstroms between:
------- .R<DA 523>.A<P 1> and .R<DA 523>.A<O1P 2>
WARNING: There is a bond of 20.147260 angstroms between:
------- .R<DA 523>.A<P 1> and .R<DA 523>.A<O2P 3>
WARNING: There is a bond of 18.218038 angstroms between:
------- .R<DG 524>.A<P 1> and .R<DG 524>.A<O1P 2>
WARNING: There is a bond of 16.330925 angstroms between:
------- .R<DG 524>.A<P 1> and .R<DG 524>.A<O2P 3>
WARNING: There is a bond of 17.148641 angstroms between:
------- .R<DG 525>.A<P 1> and .R<DG 525>.A<O1P 2>
WARNING: There is a bond of 19.160403 angstroms between:
------- .R<DG 525>.A<P 1> and .R<DG 525>.A<O2P 3>
WARNING: There is a bond of 12.952411 angstroms between:
------- .R<DG 526>.A<P 1> and .R<DG 526>.A<O1P 2>
WARNING: There is a bond of 14.615557 angstroms between:
------- .R<DG 526>.A<P 1> and .R<DG 526>.A<O2P 3>
WARNING: There is a bond of 11.766026 angstroms between:
------- .R<DT 527>.A<P 1> and .R<DT 527>.A<O1P 2>
WARNING: There is a bond of 14.071320 angstroms between:
------- .R<DT 527>.A<P 1> and .R<DT 527>.A<O2P 3>
WARNING: There is a bond of 14.702758 angstroms between:
------- .R<DT 528>.A<P 1> and .R<DT 528>.A<O1P 2>
WARNING: There is a bond of 15.622305 angstroms between:
------- .R<DT 528>.A<P 1> and .R<DT 528>.A<O2P 3>
WARNING: There is a bond of 13.134861 angstroms between:
------- .R<DA 529>.A<P 1> and .R<DA 529>.A<O1P 2>
WARNING: There is a bond of 11.959159 angstroms between:
------- .R<DA 529>.A<P 1> and .R<DA 529>.A<O2P 3>
WARNING: There is a bond of 6.545859 angstroms between:
------- .R<DG 530>.A<P 1> and .R<DG 530>.A<O1P 2>
WARNING: There is a bond of 4.293525 angstroms between:
------- .R<DG 530>.A<P 1> and .R<DG 530>.A<O2P 3>
WARNING: There is a bond of 14.023133 angstroms between:
------- .R<DG 531>.A<P 1> and .R<DG 531>.A<O1P 2>
WARNING: There is a bond of 15.170539 angstroms between:
------- .R<DG 531>.A<P 1> and .R<DG 531>.A<O2P 3>
WARNING: There is a bond of 12.847688 angstroms between:
------- .R<DG 532>.A<P 1> and .R<DG 532>.A<O1P 2>
WARNING: There is a bond of 14.748996 angstroms between:
------- .R<DG 532>.A<P 1> and .R<DG 532>.A<O2P 3>
WARNING: There is a bond of 12.040013 angstroms between:
------- .R<DA 533>.A<P 1> and .R<DA 533>.A<O1P 2>
WARNING: There is a bond of 14.059388 angstroms between:
------- .R<DA 533>.A<P 1> and .R<DA 533>.A<O2P 3>
WARNING: There is a bond of 16.238526 angstroms between:
------- .R<DA3 534>.A<P 1> and .R<DA3 534>.A<O1P 2>
WARNING: There is a bond of 17.737285 angstroms between:
------- .R<DA3 534>.A<P 1> and .R<DA3 534>.A<O2P 3>
WARNING: There is a bond of 16.348348 angstroms between:
------- .R<DG 536>.A<C2 22> and .R<DG 536>.A<N3 26>
WARNING: There is a bond of 17.639937 angstroms between:
------- .R<DG 536>.A<C6 18> and .R<DG 536>.A<N1 20>
WARNING: There is a bond of 10.824288 angstroms between:
------- .R<DG3 537>.A<C2 22> and .R<DG3 537>.A<N3 26>
WARNING: There is a bond of 12.910750 angstroms between:
------- .R<DG3 537>.A<C6 18> and .R<DG3 537>.A<N1 20>
WARNING: There is a bond of 19.771009 angstroms between:
------- .R<DG 539>.A<C2 22> and .R<DG 539>.A<N3 26>
WARNING: There is a bond of 19.824237 angstroms between:
------- .R<DG 539>.A<C6 18> and .R<DG 539>.A<N1 20>
WARNING: There is a bond of 19.167490 angstroms between:
------- .R<DG3 540>.A<C2 22> and .R<DG3 540>.A<N3 26>
WARNING: There is a bond of 21.867976 angstroms between:
------- .R<DG3 540>.A<C6 18> and .R<DG3 540>.A<N1 20>
WARNING: There is a bond of 11.993058 angstroms between:
------- .R<DG 542>.A<C2 22> and .R<DG 542>.A<N3 26>
WARNING: There is a bond of 12.077933 angstroms between:
------- .R<DG 542>.A<C6 18> and .R<DG 542>.A<N1 20>
WARNING: There is a bond of 5.803229 angstroms between:
------- .R<DG3 543>.A<C2 22> and .R<DG3 543>.A<N3 26>
WARNING: There is a bond of 8.418710 angstroms between:
------- .R<DG3 543>.A<C6 18> and .R<DG3 543>.A<N1 20>
WARNING: There is a bond of 15.974293 angstroms between:
------- .R<DG 545>.A<C2 22> and .R<DG 545>.A<N3 26>
WARNING: There is a bond of 16.777692 angstroms between:
------- .R<DG 545>.A<C6 18> and .R<DG 545>.A<N1 20>
WARNING: There is a bond of 14.823552 angstroms between:
------- .R<DG3 546>.A<C2 22> and .R<DG3 546>.A<N3 26>
WARNING: There is a bond of 15.059460 angstroms between:
------- .R<DG3 546>.A<C6 18> and .R<DG3 546>.A<N1 20>
ERROR: The unperturbed charge of the unit: -422.763000 is not integral.
WARNING: The unperturbed charge of the unit: -422.763000 is not zero.
FATAL: Atom .R<LIG 1>.A<C 1> does not have a type.
FATAL: Atom .R<LIG 8>.A<C 1> does not have a type.
FATAL: Atom .R<LIG 21>.A<C 1> does not have a type.
FATAL: Atom .R<LIG 28>.A<C 1> does not have a type.
FATAL: Atom .R<LIG 55>.A<C 1> does not have a type.
FATAL: Atom .R<LIG 83>.A<C 1> does not have a type.
FATAL: Atom .R<LIG 100>.A<H 1> does not have a type.
FATAL: Atom .R<DA3 214>.A<H5T 34> does not have a type.
FATAL: Atom .R<LIG 329>.A<N 1> does not have a type.
FATAL: Atom .R<LIG 448>.A<N 1> does not have a type.
FATAL: Atom .R<LIG 475>.A<N 1> does not have a type.
FATAL: Atom .R<DA5 510>.A<O1P 31> does not have a type.
FATAL: Atom .R<DA5 510>.A<O2P 32> does not have a type.
Failed to generate parameters
Parameter file was not saved.
Writing pdb file: 2hy9-l1-prp3.pdb
Quit
I guess that the parameter file was not saved since C1,N1,H1,O1P,O2P etc
does not have a type. I saw the leaprc.gaff but didn't find any information
regarding this.
Please help.
Asfa
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Received on Mon Apr 12 2010 - 23:30:03 PDT
