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From: laura zhang via AMBER <amber.ambermd.org>

Date: Fri, 20 Jan 2023 22:46:43 +0000

Dear Amber users,

I tried to set up a protein bound with a ligand simulation. In the tleap step, I got the following error message:

/amber20/bin/teLeap: Warning!

The unperturbed charge of the unit (-5.000000) is not zero.

FATAL: Atom .R<CARG 530>.A<HD1 29> does not have a type.

FATAL: Atom .R<CARG 530>.A<HG1 28> does not have a type.

FATAL: Atom .R<CARG 530>.A<HB1 27> does not have a type.

FATAL: Atom .R<CARG 530>.A<HN 26> does not have a type.

FATAL: Atom .R<SER 529>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 529>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 529>.A<HN 12> does not have a type.

FATAL: Atom .R<ARG 528>.A<HD1 28> does not have a type.

FATAL: Atom .R<ARG 528>.A<HG1 27> does not have a type.

FATAL: Atom .R<ARG 528>.A<HB1 26> does not have a type.

FATAL: Atom .R<ARG 528>.A<HN 25> does not have a type.

FATAL: Atom .R<CYX 527>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 527>.A<HN 11> does not have a type.

FATAL: Atom .R<CYX 526>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 526>.A<HN 11> does not have a type.

FATAL: Atom .R<ILE 525>.A<HD3 25> does not have a type.

FATAL: Atom .R<ILE 525>.A<HD2 24> does not have a type.

FATAL: Atom .R<ILE 525>.A<HD1 23> does not have a type.

FATAL: Atom .R<ILE 525>.A<CD 22> does not have a type.

FATAL: Atom .R<ILE 525>.A<HG11 21> does not have a type.

FATAL: Atom .R<ILE 525>.A<HN 20> does not have a type.

FATAL: Atom .R<ALA 524>.A<HN 11> does not have a type.

FATAL: Atom .R<VAL 523>.A<HN 17> does not have a type.

FATAL: Atom .R<ALA 522>.A<HN 11> does not have a type.

FATAL: Atom .R<THR 521>.A<HN 15> does not have a type.

FATAL: Atom .R<VAL 520>.A<HN 17> does not have a type.

FATAL: Atom .R<ALA 519>.A<HN 11> does not have a type.

FATAL: Atom .R<GLY 518>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 518>.A<HN 8> does not have a type.

FATAL: Atom .R<GLU 517>.A<HG1 18> does not have a type.

FATAL: Atom .R<GLU 517>.A<HB1 17> does not have a type.

FATAL: Atom .R<GLU 517>.A<HN 16> does not have a type.

FATAL: Atom .R<SER 516>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 516>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 516>.A<HN 12> does not have a type.

FATAL: Atom .R<THR 515>.A<HN 15> does not have a type.

FATAL: Atom .R<SER 514>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 514>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 514>.A<HN 12> does not have a type.

FATAL: Atom .R<GLY 513>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 513>.A<HN 8> does not have a type.

FATAL: Atom .R<THR 512>.A<HN 15> does not have a type.

FATAL: Atom .R<THR 511>.A<HN 15> does not have a type.

FATAL: Atom .R<SER 510>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 510>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 510>.A<HN 12> does not have a type.

FATAL: Atom .R<VAL 509>.A<HN 17> does not have a type.

FATAL: Atom .R<ASP 508>.A<HB1 14> does not have a type.

FATAL: Atom .R<ASP 508>.A<HN 13> does not have a type.

FATAL: Atom .R<ARG 507>.A<HD1 28> does not have a type.

FATAL: Atom .R<ARG 507>.A<HG1 27> does not have a type.

FATAL: Atom .R<ARG 507>.A<HB1 26> does not have a type.

FATAL: Atom .R<ARG 507>.A<HN 25> does not have a type.

FATAL: Atom .R<SER 506>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 506>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 506>.A<HN 12> does not have a type.

FATAL: Atom .R<ARG 505>.A<HD1 28> does not have a type.

FATAL: Atom .R<ARG 505>.A<HG1 27> does not have a type.

FATAL: Atom .R<ARG 505>.A<HB1 26> does not have a type.

FATAL: Atom .R<ARG 505>.A<HN 25> does not have a type.

FATAL: Atom .R<VAL 504>.A<HN 17> does not have a type.

FATAL: Atom .R<VAL 503>.A<HN 17> does not have a type.

FATAL: Atom .R<CYX 502>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 502>.A<HN 11> does not have a type.

FATAL: Atom .R<THR 501>.A<HN 15> does not have a type.

FATAL: Atom .R<ASN 500>.A<HB1 16> does not have a type.

FATAL: Atom .R<ASN 500>.A<HN 15> does not have a type.

FATAL: Atom .R<ASP 499>.A<HB1 14> does not have a type.

FATAL: Atom .R<ASP 499>.A<HN 13> does not have a type.

FATAL: Atom .R<VAL 498>.A<HN 17> does not have a type.

FATAL: Atom .R<ALA 497>.A<HN 11> does not have a type.

FATAL: Atom .R<TYR 496>.A<HB1 23> does not have a type.

FATAL: Atom .R<TYR 496>.A<HN 22> does not have a type.

FATAL: Atom .R<ALA 495>.A<HN 11> does not have a type.

FATAL: Atom .R<GLY 494>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 494>.A<HN 8> does not have a type.

FATAL: Atom .R<LEU 493>.A<HB1 21> does not have a type.

FATAL: Atom .R<LEU 493>.A<HN 20> does not have a type.

FATAL: Atom .R<VAL 492>.A<HN 17> does not have a type.

FATAL: Atom .R<HID 491>.A<HB1 19> does not have a type.

FATAL: Atom .R<HID 491>.A<HN 18> does not have a type.

FATAL: Atom .R<SER 490>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 490>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 490>.A<HN 12> does not have a type.

FATAL: Atom .R<THR 489>.A<HN 15> does not have a type.

FATAL: Atom .R<GLY 488>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 488>.A<HN 8> does not have a type.

FATAL: Atom .R<PRO 487>.A<HG1 17> does not have a type.

FATAL: Atom .R<PRO 487>.A<HB1 16> does not have a type.

FATAL: Atom .R<PRO 487>.A<HD1 15> does not have a type.

FATAL: Atom .R<LEU 486>.A<HB1 21> does not have a type.

FATAL: Atom .R<LEU 486>.A<HN 20> does not have a type.

FATAL: Atom .R<ALA 485>.A<HN 11> does not have a type.

FATAL: Atom .R<SER 484>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 484>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 484>.A<HN 12> does not have a type.

FATAL: Atom .R<CYX 483>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 483>.A<HN 11> does not have a type.

FATAL: Atom .R<GLY 482>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 482>.A<HN 8> does not have a type.

FATAL: Atom .R<THR 481>.A<HN 15> does not have a type.

FATAL: Atom .R<LEU 480>.A<HB1 21> does not have a type.

FATAL: Atom .R<LEU 480>.A<HN 20> does not have a type.

FATAL: Atom .R<THR 479>.A<HN 15> does not have a type.

FATAL: Atom .R<TRP 478>.A<HB1 26> does not have a type.

FATAL: Atom .R<TRP 478>.A<HN 25> does not have a type.

FATAL: Atom .R<GLY 477>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 477>.A<HN 8> does not have a type.

FATAL: Atom .R<GLU 476>.A<HG1 18> does not have a type.

FATAL: Atom .R<GLU 476>.A<HB1 17> does not have a type.

FATAL: Atom .R<GLU 476>.A<HN 16> does not have a type.

FATAL: Atom .R<GLU 475>.A<HG1 18> does not have a type.

FATAL: Atom .R<GLU 475>.A<HB1 17> does not have a type.

FATAL: Atom .R<GLU 475>.A<HN 16> does not have a type.

FATAL: Atom .R<CYX 474>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 474>.A<HN 11> does not have a type.

FATAL: Atom .R<ALA 473>.A<HN 11> does not have a type.

FATAL: Atom .R<VAL 472>.A<HN 17> does not have a type.

FATAL: Atom .R<THR 471>.A<HN 15> does not have a type.

FATAL: Atom .R<VAL 470>.A<HN 17> does not have a type.

FATAL: Atom .R<GLN 469>.A<HG1 20> does not have a type.

FATAL: Atom .R<GLN 469>.A<HB1 19> does not have a type.

FATAL: Atom .R<GLN 469>.A<HN 18> does not have a type.

FATAL: Atom .R<GLU 468>.A<HG1 18> does not have a type.

FATAL: Atom .R<GLU 468>.A<HB1 17> does not have a type.

FATAL: Atom .R<GLU 468>.A<HN 16> does not have a type.

FATAL: Atom .R<GLN 467>.A<HG1 20> does not have a type.

FATAL: Atom .R<GLN 467>.A<HB1 19> does not have a type.

FATAL: Atom .R<GLN 467>.A<HN 18> does not have a type.

FATAL: Atom .R<PRO 466>.A<HG1 17> does not have a type.

FATAL: Atom .R<PRO 466>.A<HB1 16> does not have a type.

FATAL: Atom .R<PRO 466>.A<HD1 15> does not have a type.

FATAL: Atom .R<ALA 465>.A<HN 11> does not have a type.

FATAL: Atom .R<PRO 464>.A<HG1 17> does not have a type.

FATAL: Atom .R<PRO 464>.A<HB1 16> does not have a type.

FATAL: Atom .R<PRO 464>.A<HD1 15> does not have a type.

FATAL: Atom .R<ILE 463>.A<HD3 25> does not have a type.

FATAL: Atom .R<ILE 463>.A<HD2 24> does not have a type.

FATAL: Atom .R<ILE 463>.A<HD1 23> does not have a type.

FATAL: Atom .R<ILE 463>.A<CD 22> does not have a type.

FATAL: Atom .R<ILE 463>.A<HG11 21> does not have a type.

FATAL: Atom .R<ILE 463>.A<HN 20> does not have a type.

FATAL: Atom .R<GLY 462>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 462>.A<HN 8> does not have a type.

FATAL: Atom .R<HID 461>.A<HB1 19> does not have a type.

FATAL: Atom .R<HID 461>.A<HN 18> does not have a type.

FATAL: Atom .R<GLU 460>.A<HG1 18> does not have a type.

FATAL: Atom .R<GLU 460>.A<HB1 17> does not have a type.

FATAL: Atom .R<GLU 460>.A<HN 16> does not have a type.

FATAL: Atom .R<LYS 459>.A<HE1 27> does not have a type.

FATAL: Atom .R<LYS 459>.A<HD1 26> does not have a type.

FATAL: Atom .R<LYS 459>.A<HG1 25> does not have a type.

FATAL: Atom .R<LYS 459>.A<HB1 24> does not have a type.

FATAL: Atom .R<LYS 459>.A<HN 23> does not have a type.

FATAL: Atom .R<VAL 458>.A<HN 17> does not have a type.

FATAL: Atom .R<LYS 457>.A<HE1 27> does not have a type.

FATAL: Atom .R<LYS 457>.A<HD1 26> does not have a type.

FATAL: Atom .R<LYS 457>.A<HG1 25> does not have a type.

FATAL: Atom .R<LYS 457>.A<HB1 24> does not have a type.

FATAL: Atom .R<LYS 457>.A<HN 23> does not have a type.

FATAL: Atom .R<CYX 456>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 456>.A<HN 11> does not have a type.

FATAL: Atom .R<GLU 455>.A<HG1 18> does not have a type.

FATAL: Atom .R<GLU 455>.A<HB1 17> does not have a type.

FATAL: Atom .R<GLU 455>.A<HN 16> does not have a type.

FATAL: Atom .R<LEU 454>.A<HB1 21> does not have a type.

FATAL: Atom .R<LEU 454>.A<HN 20> does not have a type.

FATAL: Atom .R<GLY 453>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 453>.A<HN 8> does not have a type.

FATAL: Atom .R<PRO 452>.A<HG1 17> does not have a type.

FATAL: Atom .R<PRO 452>.A<HB1 16> does not have a type.

FATAL: Atom .R<PRO 452>.A<HD1 15> does not have a type.

FATAL: Atom .R<ALA 451>.A<HN 11> does not have a type.

FATAL: Atom .R<HID 450>.A<HB1 19> does not have a type.

FATAL: Atom .R<HID 450>.A<HN 18> does not have a type.

FATAL: Atom .R<CYX 449>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 449>.A<HN 11> does not have a type.

FATAL: Atom .R<CYX 448>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 448>.A<HN 11> does not have a type.

FATAL: Atom .R<SER 447>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 447>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 447>.A<HN 12> does not have a type.

FATAL: Atom .R<ALA 446>.A<HN 11> does not have a type.

FATAL: Atom .R<HID 445>.A<HB1 19> does not have a type.

FATAL: Atom .R<HID 445>.A<HN 18> does not have a type.

FATAL: Atom .R<ILE 444>.A<HD3 25> does not have a type.

FATAL: Atom .R<ILE 444>.A<HD2 24> does not have a type.

FATAL: Atom .R<ILE 444>.A<HD1 23> does not have a type.

FATAL: Atom .R<ILE 444>.A<CD 22> does not have a type.

FATAL: Atom .R<ILE 444>.A<HG11 21> does not have a type.

FATAL: Atom .R<ILE 444>.A<HN 20> does not have a type.

FATAL: Atom .R<SER 443>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 443>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 443>.A<HN 12> does not have a type.

FATAL: Atom .R<ALA 442>.A<HN 11> does not have a type.

FATAL: Atom .R<GLU 441>.A<HG1 18> does not have a type.

FATAL: Atom .R<GLU 441>.A<HB1 17> does not have a type.

FATAL: Atom .R<GLU 441>.A<HN 16> does not have a type.

FATAL: Atom .R<ARG 440>.A<HD1 28> does not have a type.

FATAL: Atom .R<ARG 440>.A<HG1 27> does not have a type.

FATAL: Atom .R<ARG 440>.A<HB1 26> does not have a type.

FATAL: Atom .R<ARG 440>.A<HN 25> does not have a type.

FATAL: Atom .R<HID 439>.A<HB1 19> does not have a type.

FATAL: Atom .R<HID 439>.A<HN 18> does not have a type.

FATAL: Atom .R<GLY 438>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 438>.A<HN 8> does not have a type.

FATAL: Atom .R<VAL 437>.A<HN 17> does not have a type.

FATAL: Atom .R<CYX 436>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 436>.A<HN 11> does not have a type.

FATAL: Atom .R<GLN 435>.A<HG1 20> does not have a type.

FATAL: Atom .R<GLN 435>.A<HB1 19> does not have a type.

FATAL: Atom .R<GLN 435>.A<HN 18> does not have a type.

FATAL: Atom .R<ASN 434>.A<HB1 16> does not have a type.

FATAL: Atom .R<ASN 434>.A<HN 15> does not have a type.

FATAL: Atom .R<PRO 433>.A<HG1 17> does not have a type.

FATAL: Atom .R<PRO 433>.A<HB1 16> does not have a type.

FATAL: Atom .R<PRO 433>.A<HD1 15> does not have a type.

FATAL: Atom .R<GLN 432>.A<HG1 20> does not have a type.

FATAL: Atom .R<GLN 432>.A<HB1 19> does not have a type.

FATAL: Atom .R<GLN 432>.A<HN 18> does not have a type.

FATAL: Atom .R<GLY 431>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 431>.A<HN 8> does not have a type.

FATAL: Atom .R<ARG 430>.A<HD1 28> does not have a type.

FATAL: Atom .R<ARG 430>.A<HG1 27> does not have a type.

FATAL: Atom .R<ARG 430>.A<HB1 26> does not have a type.

FATAL: Atom .R<ARG 430>.A<HN 25> does not have a type.

FATAL: Atom .R<PRO 429>.A<HG1 17> does not have a type.

FATAL: Atom .R<PRO 429>.A<HB1 16> does not have a type.

FATAL: Atom .R<PRO 429>.A<HD1 15> does not have a type.

FATAL: Atom .R<ARG 428>.A<HD1 28> does not have a type.

FATAL: Atom .R<ARG 428>.A<HG1 27> does not have a type.

FATAL: Atom .R<ARG 428>.A<HB1 26> does not have a type.

FATAL: Atom .R<ARG 428>.A<HN 25> does not have a type.

FATAL: Atom .R<LEU 427>.A<HB1 21> does not have a type.

FATAL: Atom .R<LEU 427>.A<HN 20> does not have a type.

FATAL: Atom .R<VAL 426>.A<HN 17> does not have a type.

FATAL: Atom .R<PRO 425>.A<HG1 17> does not have a type.

FATAL: Atom .R<PRO 425>.A<HB1 16> does not have a type.

FATAL: Atom .R<PRO 425>.A<HD1 15> does not have a type.

FATAL: Atom .R<PRO 424>.A<HG1 17> does not have a type.

FATAL: Atom .R<PRO 424>.A<HB1 16> does not have a type.

FATAL: Atom .R<PRO 424>.A<HD1 15> does not have a type.

FATAL: Atom .R<LYS 423>.A<HE1 27> does not have a type.

FATAL: Atom .R<LYS 423>.A<HD1 26> does not have a type.

FATAL: Atom .R<LYS 423>.A<HG1 25> does not have a type.

FATAL: Atom .R<LYS 423>.A<HB1 24> does not have a type.

FATAL: Atom .R<LYS 423>.A<HN 23> does not have a type.

FATAL: Atom .R<HID 422>.A<HB1 19> does not have a type.

FATAL: Atom .R<HID 422>.A<HN 18> does not have a type.

FATAL: Atom .R<THR 421>.A<HN 15> does not have a type.

FATAL: Atom .R<GLY 420>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 420>.A<HN 8> does not have a type.

FATAL: Atom .R<LEU 419>.A<HB1 21> does not have a type.

FATAL: Atom .R<LEU 419>.A<HN 20> does not have a type.

FATAL: Atom .R<ASP 418>.A<HB1 14> does not have a type.

FATAL: Atom .R<ASP 418>.A<HN 13> does not have a type.

FATAL: Atom .R<GLU 417>.A<HG1 18> does not have a type.

FATAL: Atom .R<GLU 417>.A<HB1 17> does not have a type.

FATAL: Atom .R<GLU 417>.A<HN 16> does not have a type.

FATAL: Atom .R<VAL 416>.A<HN 17> does not have a type.

FATAL: Atom .R<GLU 415>.A<HG1 18> does not have a type.

FATAL: Atom .R<GLU 415>.A<HB1 17> does not have a type.

FATAL: Atom .R<GLU 415>.A<HN 16> does not have a type.

FATAL: Atom .R<TRP 414>.A<HB1 26> does not have a type.

FATAL: Atom .R<TRP 414>.A<HN 25> does not have a type.

FATAL: Atom .R<HID 413>.A<HB1 19> does not have a type.

FATAL: Atom .R<HID 413>.A<HN 18> does not have a type.

FATAL: Atom .R<SER 412>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 412>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 412>.A<HN 12> does not have a type.

FATAL: Atom .R<SER 411>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 411>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 411>.A<HN 12> does not have a type.

FATAL: Atom .R<CYX 410>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 410>.A<HN 11> does not have a type.

FATAL: Atom .R<GLY 409>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 409>.A<HN 8> does not have a type.

FATAL: Atom .R<THR 408>.A<HN 15> does not have a type.

FATAL: Atom .R<LEU 407>.A<HB1 21> does not have a type.

FATAL: Atom .R<LEU 407>.A<HN 20> does not have a type.

FATAL: Atom .R<VAL 406>.A<HN 17> does not have a type.

FATAL: Atom .R<HID 405>.A<HB1 19> does not have a type.

FATAL: Atom .R<HID 405>.A<HN 18> does not have a type.

FATAL: Atom .R<GLY 404>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 404>.A<HN 8> does not have a type.

FATAL: Atom .R<GLN 403>.A<HG1 20> does not have a type.

FATAL: Atom .R<GLN 403>.A<HB1 19> does not have a type.

FATAL: Atom .R<GLN 403>.A<HN 18> does not have a type.

FATAL: Atom .R<GLN 402>.A<HG1 20> does not have a type.

FATAL: Atom .R<GLN 402>.A<HB1 19> does not have a type.

FATAL: Atom .R<GLN 402>.A<HN 18> does not have a type.

FATAL: Atom .R<HID 401>.A<HB1 19> does not have a type.

FATAL: Atom .R<HID 401>.A<HN 18> does not have a type.

FATAL: Atom .R<CYX 400>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 400>.A<HN 11> does not have a type.

FATAL: Atom .R<HID 399>.A<HB1 19> does not have a type.

FATAL: Atom .R<HID 399>.A<HN 18> does not have a type.

FATAL: Atom .R<VAL 398>.A<HN 17> does not have a type.

FATAL: Atom .R<ARG 397>.A<HD1 28> does not have a type.

FATAL: Atom .R<ARG 397>.A<HG1 27> does not have a type.

FATAL: Atom .R<ARG 397>.A<HB1 26> does not have a type.

FATAL: Atom .R<ARG 397>.A<HN 25> does not have a type.

FATAL: Atom .R<THR 396>.A<HN 15> does not have a type.

FATAL: Atom .R<GLY 395>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 395>.A<HN 8> does not have a type.

FATAL: Atom .R<MET 394>.A<HG1 20> does not have a type.

FATAL: Atom .R<MET 394>.A<HB1 19> does not have a type.

FATAL: Atom .R<MET 394>.A<HN 18> does not have a type.

FATAL: Atom .R<SER 393>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 393>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 393>.A<HN 12> does not have a type.

FATAL: Atom .R<ALA 392>.A<HN 11> does not have a type.

FATAL: Atom .R<GLU 391>.A<HG1 18> does not have a type.

FATAL: Atom .R<GLU 391>.A<HB1 17> does not have a type.

FATAL: Atom .R<GLU 391>.A<HN 16> does not have a type.

FATAL: Atom .R<ALA 390>.A<HN 11> does not have a type.

FATAL: Atom .R<PRO 389>.A<HG1 17> does not have a type.

FATAL: Atom .R<PRO 389>.A<HB1 16> does not have a type.

FATAL: Atom .R<PRO 389>.A<HD1 15> does not have a type.

FATAL: Atom .R<PRO 388>.A<HG1 17> does not have a type.

FATAL: Atom .R<PRO 388>.A<HB1 16> does not have a type.

FATAL: Atom .R<PRO 388>.A<HD1 15> does not have a type.

FATAL: Atom .R<ALA 387>.A<HN 11> does not have a type.

FATAL: Atom .R<THR 386>.A<HN 15> does not have a type.

FATAL: Atom .R<HID 385>.A<HB1 19> does not have a type.

FATAL: Atom .R<HID 385>.A<HN 18> does not have a type.

FATAL: Atom .R<VAL 384>.A<HN 17> does not have a type.

FATAL: Atom .R<SER 383>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 383>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 383>.A<HN 12> does not have a type.

FATAL: Atom .R<CYX 382>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 382>.A<HN 11> does not have a type.

FATAL: Atom .R<ASN 381>.A<HB1 16> does not have a type.

FATAL: Atom .R<ASN 381>.A<HN 15> does not have a type.

FATAL: Atom .R<ALA 380>.A<HN 11> does not have a type.

FATAL: Atom .R<GLN 379>.A<HG1 20> does not have a type

I am wondering where is wrong. In fact, the protein complex in gas phase pdb file was generated without any problem in the tleap step, although the parm7 file could not be generated. The following was copied from the related tleap script:

gascomplex= combine {rec lig}

savepdb gascomplex pcsk.gas.complex.pdb

saveamberparm gascomplex pcsk.complex.parm7 pcsk.gas.complex.rst7

I am wondering where is wrong. One observation is that the original protein pdb file has the residue number starting from 2, while the pcsk.gas.complex.pdb file has the protein residue number starting from 1. Will that contribute to the error? I can attach the whole output from tleap run and the pcsk.gas.complex.pdb file if they are useful. Thank you very much.

Laura

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Received on Fri Jan 20 2023 - 15:00:03 PST

Date: Fri, 20 Jan 2023 22:46:43 +0000

Dear Amber users,

I tried to set up a protein bound with a ligand simulation. In the tleap step, I got the following error message:

/amber20/bin/teLeap: Warning!

The unperturbed charge of the unit (-5.000000) is not zero.

FATAL: Atom .R<CARG 530>.A<HD1 29> does not have a type.

FATAL: Atom .R<CARG 530>.A<HG1 28> does not have a type.

FATAL: Atom .R<CARG 530>.A<HB1 27> does not have a type.

FATAL: Atom .R<CARG 530>.A<HN 26> does not have a type.

FATAL: Atom .R<SER 529>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 529>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 529>.A<HN 12> does not have a type.

FATAL: Atom .R<ARG 528>.A<HD1 28> does not have a type.

FATAL: Atom .R<ARG 528>.A<HG1 27> does not have a type.

FATAL: Atom .R<ARG 528>.A<HB1 26> does not have a type.

FATAL: Atom .R<ARG 528>.A<HN 25> does not have a type.

FATAL: Atom .R<CYX 527>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 527>.A<HN 11> does not have a type.

FATAL: Atom .R<CYX 526>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 526>.A<HN 11> does not have a type.

FATAL: Atom .R<ILE 525>.A<HD3 25> does not have a type.

FATAL: Atom .R<ILE 525>.A<HD2 24> does not have a type.

FATAL: Atom .R<ILE 525>.A<HD1 23> does not have a type.

FATAL: Atom .R<ILE 525>.A<CD 22> does not have a type.

FATAL: Atom .R<ILE 525>.A<HG11 21> does not have a type.

FATAL: Atom .R<ILE 525>.A<HN 20> does not have a type.

FATAL: Atom .R<ALA 524>.A<HN 11> does not have a type.

FATAL: Atom .R<VAL 523>.A<HN 17> does not have a type.

FATAL: Atom .R<ALA 522>.A<HN 11> does not have a type.

FATAL: Atom .R<THR 521>.A<HN 15> does not have a type.

FATAL: Atom .R<VAL 520>.A<HN 17> does not have a type.

FATAL: Atom .R<ALA 519>.A<HN 11> does not have a type.

FATAL: Atom .R<GLY 518>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 518>.A<HN 8> does not have a type.

FATAL: Atom .R<GLU 517>.A<HG1 18> does not have a type.

FATAL: Atom .R<GLU 517>.A<HB1 17> does not have a type.

FATAL: Atom .R<GLU 517>.A<HN 16> does not have a type.

FATAL: Atom .R<SER 516>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 516>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 516>.A<HN 12> does not have a type.

FATAL: Atom .R<THR 515>.A<HN 15> does not have a type.

FATAL: Atom .R<SER 514>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 514>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 514>.A<HN 12> does not have a type.

FATAL: Atom .R<GLY 513>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 513>.A<HN 8> does not have a type.

FATAL: Atom .R<THR 512>.A<HN 15> does not have a type.

FATAL: Atom .R<THR 511>.A<HN 15> does not have a type.

FATAL: Atom .R<SER 510>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 510>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 510>.A<HN 12> does not have a type.

FATAL: Atom .R<VAL 509>.A<HN 17> does not have a type.

FATAL: Atom .R<ASP 508>.A<HB1 14> does not have a type.

FATAL: Atom .R<ASP 508>.A<HN 13> does not have a type.

FATAL: Atom .R<ARG 507>.A<HD1 28> does not have a type.

FATAL: Atom .R<ARG 507>.A<HG1 27> does not have a type.

FATAL: Atom .R<ARG 507>.A<HB1 26> does not have a type.

FATAL: Atom .R<ARG 507>.A<HN 25> does not have a type.

FATAL: Atom .R<SER 506>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 506>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 506>.A<HN 12> does not have a type.

FATAL: Atom .R<ARG 505>.A<HD1 28> does not have a type.

FATAL: Atom .R<ARG 505>.A<HG1 27> does not have a type.

FATAL: Atom .R<ARG 505>.A<HB1 26> does not have a type.

FATAL: Atom .R<ARG 505>.A<HN 25> does not have a type.

FATAL: Atom .R<VAL 504>.A<HN 17> does not have a type.

FATAL: Atom .R<VAL 503>.A<HN 17> does not have a type.

FATAL: Atom .R<CYX 502>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 502>.A<HN 11> does not have a type.

FATAL: Atom .R<THR 501>.A<HN 15> does not have a type.

FATAL: Atom .R<ASN 500>.A<HB1 16> does not have a type.

FATAL: Atom .R<ASN 500>.A<HN 15> does not have a type.

FATAL: Atom .R<ASP 499>.A<HB1 14> does not have a type.

FATAL: Atom .R<ASP 499>.A<HN 13> does not have a type.

FATAL: Atom .R<VAL 498>.A<HN 17> does not have a type.

FATAL: Atom .R<ALA 497>.A<HN 11> does not have a type.

FATAL: Atom .R<TYR 496>.A<HB1 23> does not have a type.

FATAL: Atom .R<TYR 496>.A<HN 22> does not have a type.

FATAL: Atom .R<ALA 495>.A<HN 11> does not have a type.

FATAL: Atom .R<GLY 494>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 494>.A<HN 8> does not have a type.

FATAL: Atom .R<LEU 493>.A<HB1 21> does not have a type.

FATAL: Atom .R<LEU 493>.A<HN 20> does not have a type.

FATAL: Atom .R<VAL 492>.A<HN 17> does not have a type.

FATAL: Atom .R<HID 491>.A<HB1 19> does not have a type.

FATAL: Atom .R<HID 491>.A<HN 18> does not have a type.

FATAL: Atom .R<SER 490>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 490>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 490>.A<HN 12> does not have a type.

FATAL: Atom .R<THR 489>.A<HN 15> does not have a type.

FATAL: Atom .R<GLY 488>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 488>.A<HN 8> does not have a type.

FATAL: Atom .R<PRO 487>.A<HG1 17> does not have a type.

FATAL: Atom .R<PRO 487>.A<HB1 16> does not have a type.

FATAL: Atom .R<PRO 487>.A<HD1 15> does not have a type.

FATAL: Atom .R<LEU 486>.A<HB1 21> does not have a type.

FATAL: Atom .R<LEU 486>.A<HN 20> does not have a type.

FATAL: Atom .R<ALA 485>.A<HN 11> does not have a type.

FATAL: Atom .R<SER 484>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 484>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 484>.A<HN 12> does not have a type.

FATAL: Atom .R<CYX 483>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 483>.A<HN 11> does not have a type.

FATAL: Atom .R<GLY 482>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 482>.A<HN 8> does not have a type.

FATAL: Atom .R<THR 481>.A<HN 15> does not have a type.

FATAL: Atom .R<LEU 480>.A<HB1 21> does not have a type.

FATAL: Atom .R<LEU 480>.A<HN 20> does not have a type.

FATAL: Atom .R<THR 479>.A<HN 15> does not have a type.

FATAL: Atom .R<TRP 478>.A<HB1 26> does not have a type.

FATAL: Atom .R<TRP 478>.A<HN 25> does not have a type.

FATAL: Atom .R<GLY 477>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 477>.A<HN 8> does not have a type.

FATAL: Atom .R<GLU 476>.A<HG1 18> does not have a type.

FATAL: Atom .R<GLU 476>.A<HB1 17> does not have a type.

FATAL: Atom .R<GLU 476>.A<HN 16> does not have a type.

FATAL: Atom .R<GLU 475>.A<HG1 18> does not have a type.

FATAL: Atom .R<GLU 475>.A<HB1 17> does not have a type.

FATAL: Atom .R<GLU 475>.A<HN 16> does not have a type.

FATAL: Atom .R<CYX 474>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 474>.A<HN 11> does not have a type.

FATAL: Atom .R<ALA 473>.A<HN 11> does not have a type.

FATAL: Atom .R<VAL 472>.A<HN 17> does not have a type.

FATAL: Atom .R<THR 471>.A<HN 15> does not have a type.

FATAL: Atom .R<VAL 470>.A<HN 17> does not have a type.

FATAL: Atom .R<GLN 469>.A<HG1 20> does not have a type.

FATAL: Atom .R<GLN 469>.A<HB1 19> does not have a type.

FATAL: Atom .R<GLN 469>.A<HN 18> does not have a type.

FATAL: Atom .R<GLU 468>.A<HG1 18> does not have a type.

FATAL: Atom .R<GLU 468>.A<HB1 17> does not have a type.

FATAL: Atom .R<GLU 468>.A<HN 16> does not have a type.

FATAL: Atom .R<GLN 467>.A<HG1 20> does not have a type.

FATAL: Atom .R<GLN 467>.A<HB1 19> does not have a type.

FATAL: Atom .R<GLN 467>.A<HN 18> does not have a type.

FATAL: Atom .R<PRO 466>.A<HG1 17> does not have a type.

FATAL: Atom .R<PRO 466>.A<HB1 16> does not have a type.

FATAL: Atom .R<PRO 466>.A<HD1 15> does not have a type.

FATAL: Atom .R<ALA 465>.A<HN 11> does not have a type.

FATAL: Atom .R<PRO 464>.A<HG1 17> does not have a type.

FATAL: Atom .R<PRO 464>.A<HB1 16> does not have a type.

FATAL: Atom .R<PRO 464>.A<HD1 15> does not have a type.

FATAL: Atom .R<ILE 463>.A<HD3 25> does not have a type.

FATAL: Atom .R<ILE 463>.A<HD2 24> does not have a type.

FATAL: Atom .R<ILE 463>.A<HD1 23> does not have a type.

FATAL: Atom .R<ILE 463>.A<CD 22> does not have a type.

FATAL: Atom .R<ILE 463>.A<HG11 21> does not have a type.

FATAL: Atom .R<ILE 463>.A<HN 20> does not have a type.

FATAL: Atom .R<GLY 462>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 462>.A<HN 8> does not have a type.

FATAL: Atom .R<HID 461>.A<HB1 19> does not have a type.

FATAL: Atom .R<HID 461>.A<HN 18> does not have a type.

FATAL: Atom .R<GLU 460>.A<HG1 18> does not have a type.

FATAL: Atom .R<GLU 460>.A<HB1 17> does not have a type.

FATAL: Atom .R<GLU 460>.A<HN 16> does not have a type.

FATAL: Atom .R<LYS 459>.A<HE1 27> does not have a type.

FATAL: Atom .R<LYS 459>.A<HD1 26> does not have a type.

FATAL: Atom .R<LYS 459>.A<HG1 25> does not have a type.

FATAL: Atom .R<LYS 459>.A<HB1 24> does not have a type.

FATAL: Atom .R<LYS 459>.A<HN 23> does not have a type.

FATAL: Atom .R<VAL 458>.A<HN 17> does not have a type.

FATAL: Atom .R<LYS 457>.A<HE1 27> does not have a type.

FATAL: Atom .R<LYS 457>.A<HD1 26> does not have a type.

FATAL: Atom .R<LYS 457>.A<HG1 25> does not have a type.

FATAL: Atom .R<LYS 457>.A<HB1 24> does not have a type.

FATAL: Atom .R<LYS 457>.A<HN 23> does not have a type.

FATAL: Atom .R<CYX 456>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 456>.A<HN 11> does not have a type.

FATAL: Atom .R<GLU 455>.A<HG1 18> does not have a type.

FATAL: Atom .R<GLU 455>.A<HB1 17> does not have a type.

FATAL: Atom .R<GLU 455>.A<HN 16> does not have a type.

FATAL: Atom .R<LEU 454>.A<HB1 21> does not have a type.

FATAL: Atom .R<LEU 454>.A<HN 20> does not have a type.

FATAL: Atom .R<GLY 453>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 453>.A<HN 8> does not have a type.

FATAL: Atom .R<PRO 452>.A<HG1 17> does not have a type.

FATAL: Atom .R<PRO 452>.A<HB1 16> does not have a type.

FATAL: Atom .R<PRO 452>.A<HD1 15> does not have a type.

FATAL: Atom .R<ALA 451>.A<HN 11> does not have a type.

FATAL: Atom .R<HID 450>.A<HB1 19> does not have a type.

FATAL: Atom .R<HID 450>.A<HN 18> does not have a type.

FATAL: Atom .R<CYX 449>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 449>.A<HN 11> does not have a type.

FATAL: Atom .R<CYX 448>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 448>.A<HN 11> does not have a type.

FATAL: Atom .R<SER 447>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 447>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 447>.A<HN 12> does not have a type.

FATAL: Atom .R<ALA 446>.A<HN 11> does not have a type.

FATAL: Atom .R<HID 445>.A<HB1 19> does not have a type.

FATAL: Atom .R<HID 445>.A<HN 18> does not have a type.

FATAL: Atom .R<ILE 444>.A<HD3 25> does not have a type.

FATAL: Atom .R<ILE 444>.A<HD2 24> does not have a type.

FATAL: Atom .R<ILE 444>.A<HD1 23> does not have a type.

FATAL: Atom .R<ILE 444>.A<CD 22> does not have a type.

FATAL: Atom .R<ILE 444>.A<HG11 21> does not have a type.

FATAL: Atom .R<ILE 444>.A<HN 20> does not have a type.

FATAL: Atom .R<SER 443>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 443>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 443>.A<HN 12> does not have a type.

FATAL: Atom .R<ALA 442>.A<HN 11> does not have a type.

FATAL: Atom .R<GLU 441>.A<HG1 18> does not have a type.

FATAL: Atom .R<GLU 441>.A<HB1 17> does not have a type.

FATAL: Atom .R<GLU 441>.A<HN 16> does not have a type.

FATAL: Atom .R<ARG 440>.A<HD1 28> does not have a type.

FATAL: Atom .R<ARG 440>.A<HG1 27> does not have a type.

FATAL: Atom .R<ARG 440>.A<HB1 26> does not have a type.

FATAL: Atom .R<ARG 440>.A<HN 25> does not have a type.

FATAL: Atom .R<HID 439>.A<HB1 19> does not have a type.

FATAL: Atom .R<HID 439>.A<HN 18> does not have a type.

FATAL: Atom .R<GLY 438>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 438>.A<HN 8> does not have a type.

FATAL: Atom .R<VAL 437>.A<HN 17> does not have a type.

FATAL: Atom .R<CYX 436>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 436>.A<HN 11> does not have a type.

FATAL: Atom .R<GLN 435>.A<HG1 20> does not have a type.

FATAL: Atom .R<GLN 435>.A<HB1 19> does not have a type.

FATAL: Atom .R<GLN 435>.A<HN 18> does not have a type.

FATAL: Atom .R<ASN 434>.A<HB1 16> does not have a type.

FATAL: Atom .R<ASN 434>.A<HN 15> does not have a type.

FATAL: Atom .R<PRO 433>.A<HG1 17> does not have a type.

FATAL: Atom .R<PRO 433>.A<HB1 16> does not have a type.

FATAL: Atom .R<PRO 433>.A<HD1 15> does not have a type.

FATAL: Atom .R<GLN 432>.A<HG1 20> does not have a type.

FATAL: Atom .R<GLN 432>.A<HB1 19> does not have a type.

FATAL: Atom .R<GLN 432>.A<HN 18> does not have a type.

FATAL: Atom .R<GLY 431>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 431>.A<HN 8> does not have a type.

FATAL: Atom .R<ARG 430>.A<HD1 28> does not have a type.

FATAL: Atom .R<ARG 430>.A<HG1 27> does not have a type.

FATAL: Atom .R<ARG 430>.A<HB1 26> does not have a type.

FATAL: Atom .R<ARG 430>.A<HN 25> does not have a type.

FATAL: Atom .R<PRO 429>.A<HG1 17> does not have a type.

FATAL: Atom .R<PRO 429>.A<HB1 16> does not have a type.

FATAL: Atom .R<PRO 429>.A<HD1 15> does not have a type.

FATAL: Atom .R<ARG 428>.A<HD1 28> does not have a type.

FATAL: Atom .R<ARG 428>.A<HG1 27> does not have a type.

FATAL: Atom .R<ARG 428>.A<HB1 26> does not have a type.

FATAL: Atom .R<ARG 428>.A<HN 25> does not have a type.

FATAL: Atom .R<LEU 427>.A<HB1 21> does not have a type.

FATAL: Atom .R<LEU 427>.A<HN 20> does not have a type.

FATAL: Atom .R<VAL 426>.A<HN 17> does not have a type.

FATAL: Atom .R<PRO 425>.A<HG1 17> does not have a type.

FATAL: Atom .R<PRO 425>.A<HB1 16> does not have a type.

FATAL: Atom .R<PRO 425>.A<HD1 15> does not have a type.

FATAL: Atom .R<PRO 424>.A<HG1 17> does not have a type.

FATAL: Atom .R<PRO 424>.A<HB1 16> does not have a type.

FATAL: Atom .R<PRO 424>.A<HD1 15> does not have a type.

FATAL: Atom .R<LYS 423>.A<HE1 27> does not have a type.

FATAL: Atom .R<LYS 423>.A<HD1 26> does not have a type.

FATAL: Atom .R<LYS 423>.A<HG1 25> does not have a type.

FATAL: Atom .R<LYS 423>.A<HB1 24> does not have a type.

FATAL: Atom .R<LYS 423>.A<HN 23> does not have a type.

FATAL: Atom .R<HID 422>.A<HB1 19> does not have a type.

FATAL: Atom .R<HID 422>.A<HN 18> does not have a type.

FATAL: Atom .R<THR 421>.A<HN 15> does not have a type.

FATAL: Atom .R<GLY 420>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 420>.A<HN 8> does not have a type.

FATAL: Atom .R<LEU 419>.A<HB1 21> does not have a type.

FATAL: Atom .R<LEU 419>.A<HN 20> does not have a type.

FATAL: Atom .R<ASP 418>.A<HB1 14> does not have a type.

FATAL: Atom .R<ASP 418>.A<HN 13> does not have a type.

FATAL: Atom .R<GLU 417>.A<HG1 18> does not have a type.

FATAL: Atom .R<GLU 417>.A<HB1 17> does not have a type.

FATAL: Atom .R<GLU 417>.A<HN 16> does not have a type.

FATAL: Atom .R<VAL 416>.A<HN 17> does not have a type.

FATAL: Atom .R<GLU 415>.A<HG1 18> does not have a type.

FATAL: Atom .R<GLU 415>.A<HB1 17> does not have a type.

FATAL: Atom .R<GLU 415>.A<HN 16> does not have a type.

FATAL: Atom .R<TRP 414>.A<HB1 26> does not have a type.

FATAL: Atom .R<TRP 414>.A<HN 25> does not have a type.

FATAL: Atom .R<HID 413>.A<HB1 19> does not have a type.

FATAL: Atom .R<HID 413>.A<HN 18> does not have a type.

FATAL: Atom .R<SER 412>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 412>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 412>.A<HN 12> does not have a type.

FATAL: Atom .R<SER 411>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 411>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 411>.A<HN 12> does not have a type.

FATAL: Atom .R<CYX 410>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 410>.A<HN 11> does not have a type.

FATAL: Atom .R<GLY 409>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 409>.A<HN 8> does not have a type.

FATAL: Atom .R<THR 408>.A<HN 15> does not have a type.

FATAL: Atom .R<LEU 407>.A<HB1 21> does not have a type.

FATAL: Atom .R<LEU 407>.A<HN 20> does not have a type.

FATAL: Atom .R<VAL 406>.A<HN 17> does not have a type.

FATAL: Atom .R<HID 405>.A<HB1 19> does not have a type.

FATAL: Atom .R<HID 405>.A<HN 18> does not have a type.

FATAL: Atom .R<GLY 404>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 404>.A<HN 8> does not have a type.

FATAL: Atom .R<GLN 403>.A<HG1 20> does not have a type.

FATAL: Atom .R<GLN 403>.A<HB1 19> does not have a type.

FATAL: Atom .R<GLN 403>.A<HN 18> does not have a type.

FATAL: Atom .R<GLN 402>.A<HG1 20> does not have a type.

FATAL: Atom .R<GLN 402>.A<HB1 19> does not have a type.

FATAL: Atom .R<GLN 402>.A<HN 18> does not have a type.

FATAL: Atom .R<HID 401>.A<HB1 19> does not have a type.

FATAL: Atom .R<HID 401>.A<HN 18> does not have a type.

FATAL: Atom .R<CYX 400>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 400>.A<HN 11> does not have a type.

FATAL: Atom .R<HID 399>.A<HB1 19> does not have a type.

FATAL: Atom .R<HID 399>.A<HN 18> does not have a type.

FATAL: Atom .R<VAL 398>.A<HN 17> does not have a type.

FATAL: Atom .R<ARG 397>.A<HD1 28> does not have a type.

FATAL: Atom .R<ARG 397>.A<HG1 27> does not have a type.

FATAL: Atom .R<ARG 397>.A<HB1 26> does not have a type.

FATAL: Atom .R<ARG 397>.A<HN 25> does not have a type.

FATAL: Atom .R<THR 396>.A<HN 15> does not have a type.

FATAL: Atom .R<GLY 395>.A<HA1 9> does not have a type.

FATAL: Atom .R<GLY 395>.A<HN 8> does not have a type.

FATAL: Atom .R<MET 394>.A<HG1 20> does not have a type.

FATAL: Atom .R<MET 394>.A<HB1 19> does not have a type.

FATAL: Atom .R<MET 394>.A<HN 18> does not have a type.

FATAL: Atom .R<SER 393>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 393>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 393>.A<HN 12> does not have a type.

FATAL: Atom .R<ALA 392>.A<HN 11> does not have a type.

FATAL: Atom .R<GLU 391>.A<HG1 18> does not have a type.

FATAL: Atom .R<GLU 391>.A<HB1 17> does not have a type.

FATAL: Atom .R<GLU 391>.A<HN 16> does not have a type.

FATAL: Atom .R<ALA 390>.A<HN 11> does not have a type.

FATAL: Atom .R<PRO 389>.A<HG1 17> does not have a type.

FATAL: Atom .R<PRO 389>.A<HB1 16> does not have a type.

FATAL: Atom .R<PRO 389>.A<HD1 15> does not have a type.

FATAL: Atom .R<PRO 388>.A<HG1 17> does not have a type.

FATAL: Atom .R<PRO 388>.A<HB1 16> does not have a type.

FATAL: Atom .R<PRO 388>.A<HD1 15> does not have a type.

FATAL: Atom .R<ALA 387>.A<HN 11> does not have a type.

FATAL: Atom .R<THR 386>.A<HN 15> does not have a type.

FATAL: Atom .R<HID 385>.A<HB1 19> does not have a type.

FATAL: Atom .R<HID 385>.A<HN 18> does not have a type.

FATAL: Atom .R<VAL 384>.A<HN 17> does not have a type.

FATAL: Atom .R<SER 383>.A<HG1 14> does not have a type.

FATAL: Atom .R<SER 383>.A<HB1 13> does not have a type.

FATAL: Atom .R<SER 383>.A<HN 12> does not have a type.

FATAL: Atom .R<CYX 382>.A<HB1 12> does not have a type.

FATAL: Atom .R<CYX 382>.A<HN 11> does not have a type.

FATAL: Atom .R<ASN 381>.A<HB1 16> does not have a type.

FATAL: Atom .R<ASN 381>.A<HN 15> does not have a type.

FATAL: Atom .R<ALA 380>.A<HN 11> does not have a type.

FATAL: Atom .R<GLN 379>.A<HG1 20> does not have a type

I am wondering where is wrong. In fact, the protein complex in gas phase pdb file was generated without any problem in the tleap step, although the parm7 file could not be generated. The following was copied from the related tleap script:

gascomplex= combine {rec lig}

savepdb gascomplex pcsk.gas.complex.pdb

saveamberparm gascomplex pcsk.complex.parm7 pcsk.gas.complex.rst7

I am wondering where is wrong. One observation is that the original protein pdb file has the residue number starting from 2, while the pcsk.gas.complex.pdb file has the protein residue number starting from 1. Will that contribute to the error? I can attach the whole output from tleap run and the pcsk.gas.complex.pdb file if they are useful. Thank you very much.

Laura

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Received on Fri Jan 20 2023 - 15:00:03 PST

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